TW201938791A - Expression vector production and high-throughput cell screening - Google Patents

Abstract

The present invention relates inter alia to expression vector production as well as application to the production of host cells for protein repertoire expression and high-throughput screening. The invention also relates to primers useful for PCR amplification of nucleotide sequences encoding human antibody variable domains.

Description

   Performance vector production and high-throughput cell screening        Field of invention    

The invention is particularly related to the production of expression vectors and the application to host cells for protein library performance and high-throughput screening. The invention also relates to nucleic acids, PCR primers and mixtures useful for PCR amplification of nucleotide sequences encoding human antibody variable domains or homologous recombination with immunoglobulin (Ig) loci in cells.

    Background of the invention    

This technique recognizes the desire to screen cells or protein libraries to identify proteins of interest (POI) or cells expressing these proteins. For example, the present technique includes techniques for screening B cells and antibody libraries in order to identify one or more cells that exhibit antibodies exhibiting a desired characteristic (typically specific antigen binding). Screening is not limited to antibody screening, but may also be suitable for screening other types of protein sets for one or more desired characteristics.

To express a protein library, the corresponding nucleotide sequence can be cloned into individual expression vectors and introduced (eg, transfected) into a host cell that can express the protein. Generally, molecular colony lines are used to colonize protein coding sequences from a pool into host cells. Molecular colony has been applied to B cell (lymphocyte) screening technology, in which B cell lines are expanded by culture and sorted into single cells (for example, using hemolytic spot detection or fluorescent foci assay), The antibody chain (or variable region) mRNA derived from the sorted cells is reverse-transcribed and amplified using RT-PCR, and the amplified DNA is subjected to molecular colonization to introduce the antibody chain coding sequence into a nucleic acid vector, and the The vector is then introduced into the host cell for transient expression (where the vector is an episomal form), or for stable expression (by random incorporation into the host cell genome). See, for example, "Proc Natl Acad Sci US A. 1996 Jul 23; 93 (15): 7843-8, A novel strategy for generating monoclonal antibodies from single, isolated lymphocytes producing antibodies of defined specificities" by JS Babcook et al. (Referred to as SLAM technology), and "Doi: 10.1016 / j.jala.2009.05.004 Journal of Laboratory Automation October 2009 vol.14 no.5 303-307, High-Throughput Screening for High Affinity" by S Tickle et al. Antibodies ", (known as UCB SLAM technology).

Molecular colonization involves the amplification of cDNA (produced by RT-PCR of POI mRNA) with primers carrying restriction endonuclease colonization sites. This will result in a PCR product where each POI nucleotide sequence is pinched by a restriction site. The PCR product is then digested with appropriate restriction enzymes and subcloned by conjugation into an empty expression vector that provides a promoter and polyadenylic acid signal and carries a selection marker. The ligated product is then transformed into E. coli, and the selection line is selected by the presence of a marker. It is necessary to confirm and select the selected plant with the correct sequence insertion by the laborious restriction map and the sequence of the selected plants. Each single correct cloned expression vector is then individually purified from E. coli and transfected into a host cell (eg, CHO or HEK293 mammalian cells) for transient or stable performance.

Molecular breeding is therefore a laborious technique involving multiple steps and is not very suitable for high throughput.

Transient performance, such as from a linear performance cassette, is usually limited, while stable performance is better for long-term performance. For stable performance, the POI coding sequence of interest is typically inserted into the mammalian genome (ie, randomly incorporated into the genome) by the classical incorporation method of spontaneous incorporation of foreign DNA. This approach often results in significant transcriptional changes (and therefore unpredictable and inconsistent POI performance) as a result of differences in transgenic copy numbers and incorporation sites (see Henikoff S, "Position effect and related, 1992 phenomena, Curr Opin Genet Dev 2 (6): 907-912 ";" The variegating transgenes, Boessays 18 (11): 919-923 "by Martin DI and Whitelaw E in 1996; and Whitelaw E and others in 2001 "Epigenetic effects on transgene expression, Methods Mol Biol. 158: 351-368)." In addition, transgenic fragments incorporated in this manner are often found to be inserted as concatemers, which may cause gene inactivation by duplication-induced gene silencing (see Garrick D et al., 1998, "Repeat-induced gene silencing in mammals, Nat Genet 18 (1): 56-59 ";and" Evidence of repeat-induced gene silencing in cultured Mammalian cells: activation of tandem repeats of transfected genes, Exp Cell Res "by McBurney MW et al., 2002 274 (1): 1-8 "). These problems hinder the production of POI banks and cell populations used to express such POI banks.

Many techniques exist for generating monoclonal antibodies (mAb) from humans or transgenic animals carrying an antibody library. In general, mAbs are obtained from immortalized B cells, either by fusion (fusion tumor technology) or by transformation (virus transfection or oncogene transformation). However, these cell immortalization methods are not suitable for comprehensive screening of large antibody libraries because they are highly biased, inefficient, and typically only sample a small fraction of the available libraries (typically less than, for example, from 0.1% of B cell bank (immortalized cells / imported cells) obtained from immunized mice). The use of alternative screening methods that do not require immortality is therefore attractive, but current technologies face the problems described above.

    Summary of invention    

The invention addresses the need for carrier production technology that is suitable for reliable production of high-throughput, suitable for storage and screening, especially those with potential for automation.

Therefore, the first configuration of the present invention provides:-at a first level, a method for producing a cell encoding a protein of interest (POI) library, the method comprising: a) providing a population of cells representing a POI library; b) analysis Selecting the cell population to generate a single cell population that is sorted, each cell containing a nucleic acid encoding a different POI; c) amplifying the nucleic acid contained in the single cell population that is sorted to produce a sorted cell population Amplified nucleic acid library encoding POI; d) modifying the sorted, amplified POI-encoding nucleic acid derived from step (c) to generate a sorted performance cassette library, each cassette containing a nucleotide encoding a POI Sequence and one or more regulatory elements for expressing the POI; and e) transplanting the POI performance cassette from the cassette library to a sorted host cell population while maintaining the POI performance cassette sorting and generating The host cell bank is sorted once the POI bank is sorted.

In one embodiment, the sorting in step (e) is maintained by providing the library in a number of relative positions and a container that is generally arranged to be fixed. This enables the methods of the invention to be processed and automated at high throughput, for example, for efficient and rapid cell screening to select one or more POI sequences of interest. Additionally or alternatively, the transgenic lines expressing the cassettes in step (e) are performed by batch transplantation, and this also enables the method of the present invention to be processed and automated at high throughput.

In a second level, an automated device for performing the foregoing method, the device comprising a) a tool for holding a single cell population sorted in one of several containers, wherein each single cell line is in a separate container Each cell contains a nucleic acid encoding a separate POI; b) a tool for delivering PCR reagents to a container for amplifying the nucleic acids contained in the sorted single cell population to generate a sorted Amplify a nucleic acid library; c) a tool for delivering reagents to a container for modifying a sorted amplified POI-encoding nucleic acid to generate a sorted library of performance cassettes, each cassette containing a nucleotide encoding a POI The sequence and one or more regulatory elements for expressing the POI; d) a tool for holding a sorted host cell population in several containers; e) for transplanting POI expression from the cassette library A cassette to a tool for sorting host cell populations in the container, while maintaining the POI performance cassette sorting; and f) a tool for performing transfection of the performance cassette to host cells in the container, to Generation of sorted hosts that represent sorted POI libraries Cell bank.

The second configuration of the present invention provides:-at a first level, a performance cassette for expressing a POI in a host cell, the cassette being provided by a linear nucleic acid comprising a transposon, the transposon comprising 5 ' -And 3'-terminal transposable elements, accompanied by a POI-encoding nucleotide sequence between the transposable elements and regulatory elements (such as) for the performance of POI.

On the second level, once the sorted expression cassette family encodes a POI library corresponding to the POI represented by a cell population, each cassette contains a nucleotide sequence encoding a member of the POI library, And one or more regulatory elements for POI performance, wherein each of the cassettes contains the arrangement (in the 5 'to 3' direction): transposable element-[POI nucleotide sequence and regulatory elements (etc. )]-Transposable elements, and performance cassettes used to express POIs derived from different cells are separated from each other in this sorted population (eg, in different holes in a plate).

In the third level, a method for making a transposer comprising a nucleotide sequence of interest (NOI) is provided. The method includes a. Providing a first nucleotide sequence comprising (in the 5 ′ end to the 3 ′ end direction) A , B and C, where A is a first homologous sequence, B is a nucleotide sequence containing the NOI, and C is a second homologous sequence; b. Providing a first template nucleotide The sequence includes (in the 5 ′ end to the 3 ′ end direction) W and X, wherein W is a nucleotide sequence including a first transposer element, and X is a third homologous sequence; and c. Provides A second template nucleotide sequence comprising (from the 5 ′ end to the 3 ′ end) Y and Z, wherein Y is a fourth homologous sequence, and Z is a nucleoside comprising a second transposon element Acid sequence; and any of the following d. (I) mixing the first nucleotide sequence with the first template to hybridize the first and third homology arms together and perform nucleic acid amplification and extension, and use the A first template extending the first nucleotide sequence to produce a first extended nucleotide sequence (first ENS), which includes (in the 5 ′ to 3 ′ direction) W, B, and C; and (ii) the first ENS and the second template Hybridization to hybridize the second and fourth homology arms together and perform nucleic acid amplification and extension to extend the first ENS to generate a second ENS, which includes (in the 5 'end to the 3' end direction) W, B and Z; or (ii) mixing the first nucleotide sequence with the second template to hybridize the second and fourth homology arms together and performing nucleic acid amplification and extension to extend the second template using the A first nucleotide sequence to generate a third extended nucleotide sequence (third ENS), which includes (in the 5 'to 3' direction) A, B, and Z; and (ii) the A third ENS is mixed with the first template to hybridize the first and third homology arms together and perform nucleic acid amplification and extension to extend the third ENS to generate a fourth ENS, which contains (at 5 ' End to 3 ′ end direction) W, B and Z; or (iii) mixing the first nucleotide sequence with the first and second templates to hybridize the first and third homology arms together, and hybridize The second and fourth homology arms are taken together, and nucleic acid amplification and extension are performed to extend the first nucleotide sequence using the second template to generate a fifth ENS, which contains (from the 5 'end to 3 ' Direction) W, B, and Z; and e. Separate ENS including (in the 5 ′ end to the 3 ′ end direction) one of W, B, and Z, thereby generating a separate transposon that contains one of the NOIs pinched by the transposer element; And f. Optionally introducing an isolated transposon into a recipient cell such that the transposon is incorporated into the genome of the cell.

A third configuration of the present invention provides:-a method of producing a host cell for expressing a POI, the method comprising a. Providing at least a first and a second performance cassette, wherein each performance cassette comprises i. A first An incorporated element and a second incorporated element 3 'of the first incorporated element nucleotide sequence; and ii. A nucleotide sequence encoding a POI between the incorporated elements and one or more Express the regulatory elements of the POI; iii. The incorporated elements are capable of pre-determining a nucleotide sequence motif by recognizing a nucleic acid and inserted into the nucleic acid using an incorporated enzyme; b. Providing a host cell Its genome contains several motifs; and c. Introducing the first and second expression cassettes into the host cell simultaneously or sequentially, wherein each cassette is based on a motif gene incorporated into the host cell Within the host cell genome for expression of POI by the host cell; and d. Optionally producing a cell line that exhibits POI in a step comprising culturing the host cell.

The fourth configuration of the present invention provides:-A nucleic acid mixture comprising a first isolated nucleic acid and a second isolated nucleic acid, wherein the first nucleic acid line is capable of hybridizing to a human antibody V region comprising a target nucleic acid The 5′-end UTR sequence, wherein the gene encodes a human V region; and the second nucleic acid line is capable of hybridizing to a second sequence, wherein the second sequence is included in the target nucleic acid and is between the UTR sequence 3 'end, wherein the first isolated nucleic acid comprises a sequence that is at least 90% identical to a sequence selected from the group consisting of sequence identification number: 1-47.

A nucleic acid mixture comprising a first isolated nucleic acid and a second isolated nucleic acid, wherein the nucleic acids are different and are selected from nucleic acids and contain at least 90% identical to those selected from the group consisting of sequence identification numbers: 1-47 A sequencer of one of the groups.

A method of amplifying a library of human variable region sequences using one or more of the sequences.

FIG. 1A is a schematic diagram illustrating one non-limiting example of the method of the present invention for generating an antibody binding site (POI) library in a host cell (such as CHO or HEK293 cells).

FIG. 1B is an alternative schematic diagram illustrating one non-limiting example of the method of the present invention for generating an antibody binding site (POI) library in a host cell (such as CHO or HEK293 cells).

Figure 2: Examples of gating strategies for different B-cell populations. (a) A first-class cytometer contour plot shows an example of gating of the CD38 + CD95 + memory cell population after excluding IgM and IgD B cells. (b) Each self-memory cell that is positive for CD19 (Pacific Blue) and antigen (ovalbumin-AlexaFluor-488) is then sorted into separate wells in a 96-well plate.

Figure 3: A flowchart summarizing high-throughput antibody production from a single B cell. Single cell-based cDNA synthesis was performed using constant region-specific primers. A V gene-specific primer mix of a heavy chain and a light chain with a human cytomegalovirus (hCMV) promoter fragment at the 5 'end was used in the first round of PCR to amplify the V gene fragment. A universal forward primer line and a reverse nested primer adhered to the hCMV tag were used in the constant region of the second round of PCR. The amplified products are then bridged to a linear Ig-cassette with a 5 'PB LTR-CMV promoter and a constant region-polyadenylation signal-3' PB LTR.

Figure 4: Manufacturing of heavy and light chain expression constructs by bridge PCR. (a) amplification of a single cell from a V _H and V _L gene segments of the ingot phenanthrene bromide stained agarose gel of acetate. Each lane contains 10 μL of 30 μL of V _H + V _L second round PCR products. (b) Aphenose bromide stained agarose gel shows the results of the bridge PCR. Each lane contains 10 μL of 30 μL bridged product for Ig-expression. This negative control group showed Ig-cages for heavy and light chains. Representative PCR products from a high-throughput 96-well PCR platform are shown here.

Figure 5: Analysis of the antibody sequence derived from item 1 of this sorted Ag-specific single B cell. The antibody sequences expressed by B cells are arranged by the heavy chain V gene family conventions and clustered to generate the displayed evolutionary tree.

Figure 6: An example of a cluster family showing affinity maturation via high mutations in both apparent affinity and neutralizing potency. CNROR: Unable to resolve level.

Figure 7: Performance boost by piggyBac indexing subsystem. The antibody expression of this transfected bridged PCR product in HEK293 cells was tested using co-transfection: with different amounts of PBase: 0; 20; 100; 500ng / well. The supernatant was collected in each hole on day 0; day 2; and day 5. The data shows that the indexing subsystem improves performance 2-4 times on the 5th day.

Figure 8: Example of quantification of IgG concentration in supernatants of HEK293 cells transfected with bridge PCR products. This concentration was determined by a sandwich ELISA on the eighth day after transfection. The concentration is from about 200 ng / mL to 3000 ng / mL, and the concentration in this range can be compared with the concentration in the supernatant of the hybridoma technique of the prior art.

Figures 9A and B: Representative SPR spectra of antibodies bound to ovalbumin. About two-thirds of the tested antibodies showed evidence of binding to the antigen, accompanied by range-differentiating differential binding affinity and kinetics.

Figure 10: Apparent affinity of antibodies against two different target antigens. A range of conjugates (hollow) and functional neutralizers (solid) were detected with the highest affinity detected in the pico-molar range. This experiment confirms that our single B cell colony technology is a powerful tool in the recognition and acquisition of high affinity and functionally competent antibodies.

    Detailed description of the invention    

FIG. 1 is a schematic diagram illustrating an example of a method for producing an antibody binding site (POI) library in a host cell (for example, CHO or HEK293 cells) according to the present invention, which is useful in a B cell screening process. In a host database system cell 1 end of the schematic diagram of the production of useful, since the cell performance can be determined antibody binding sites antigen screening (e.g. V _H / V _L pairs) for a pre to identify whichever cells showed interest Binding site. This therefore enables genotype-to-phenotype linkage, allowing identification of a nucleotide sequence encoding a binding site of interest. This nucleotide sequence can then be used to construct a cell line for stable production of the desired antibody, for example, to produce a pharmaceutical or diagnostic or research reagent antibody that targets the predetermined antigen. In one example, the host cell produced at the end of the schematic diagram of FIG. 1 itself is a cell that stably expresses the binding site, and this gives a convenient and effective stable cell line for long-term manufacturing of the binding site. The possibility of its generation. As discussed further below, in one example, site-mediated insertion of a POI-encoded expression cassette can be performed in a host cell, which provides the added advantage that this stable POI performance avoids random incorporation and concatenation.

Although examples are provided from the viewpoint of antibody binding sites, antibody variable domains, and antibody chains, the present invention is not limited to such proteins. In this sense, the invention is applicable to any protein of interest (POI). In this context, the term "protein" also includes peptides and peptides of interest, as well as proteins or peptide fragments or domains.

Returning to the non-limiting example of FIG. 1, in the first step, a desired B cell population is provided, which can be a germ cell, a memory cell, a plasmablast, a plasma cell, or generally an antibody Secretory cells (ASC), or a mixture of two or more of these B cell types. Those skilled in the art are familiar with the selection of this ethnic group, for example, using cell surface markers, optionally with FACS. Such markers may be selected from CD19, IgM, IgD, CD30, and CD95, for example, and may include a combination of one or more of these (e.g., 1, 2, 3, 4), or may include these markers All one combination. Cells with these markers may be stained, for example, by any small molecule fluorophore that can be detected by a cell sorting system, such as Alexa-488, Alexa-647, Pacific Blue, R-phycoerythrin, fluorescent Photon isothiocyanate or isophycocyanin, optionally conjugated to a cyanine dye, such as Cy7. The B cell population can be generated in a preliminary step by isolation from one or more animals, such as mice, rats or human or non-human animals, for example animals that have been immunized with a target antigen. Therefore, the method of the present invention is useful for screening B cell populations to identify one or more POI sequences derived from a B cell, wherein the POI binds to a target antigen with a desired characteristic. Such characteristics are, for example, binding to the target antigen and / or a structurally related, homologous or heterologous antigen (e.g., an antigen from a different species); and / or binding one of the desired affinities Antigen; and / or compete with a known antibody to bind a predetermined antigen (eg, the target antigen); and / or bind a predetermined epitope.

Optionally, the desired B cell population (e.g., plasmablasts or plasma cells) can be selected by performing antigen-specific cell sorting using techniques known in the art (e.g., see Jin, A, etc.) In "Nature Medicine, 2009, 15 (9): 1088-1093"). The output is a B-cell population that exhibits specific binding to an antibody-binding site of a predetermined target antigen. The inventors have found that it is advantageous to perform this step to simplify the entire B cell screening process, thereby allowing efficient and high-throughput screening.

Generally, antigen-specific GC (reproductive center) or memory B cells can be captured by marker antigens because they are manifested as transmembrane antibodies on the cell surface. The antigen may be fluorescently labeled (for example, any small molecule fluorophore that can be detected by a cell sorting system, such as Alexa-488, Alexa-647, Pacific Blue, R-phycoerythrin, fluorescent Isothiocyanate or isophycocyanin, optionally conjugated to a cyanine dye, such as Cy7). If the B cell population has been pre-stained for initial selection, it is advantageous to use a fluorophore that has an emission wavelength different from the fluorophore used in the initial selection in order to facilitate the sorting Process, such as using FACS. In an alternative, the cells may be simultaneously stained for the presence of cell selectable markers and screened for VLPs that bind to the fluorescent antigen / owning antigen. Without being limited by theory, it is believed that, on the other hand, plasmablasts or plasma cells will not be easily captured by a marker antigen because of the dominant manifestation of their secreted antibodies.

In an alternative embodiment, the antigen may be captured as a virus-like particle (VLP) with a recombinant antigen on its surface. VLPs may be produced from CHO cells, KEK cells, mouse embryo fibroblasts (MEF), or other mammalian cell lines, with recombinant antigens, retroviral gag proteins, and MA-GFP (p15-GFP fusion proteins of gag matrix fragments) ) Common performance. The expression of gag protein allows VLPs to sprout from the cells, and MA-GFP marks the VLP for fluorescent detection. Both gag and MA-GFP proteins bind to the inner surface of the plasma membrane, and the recombinant antigen is on the surface of the VLP. The antigenic line on the VLP is presented in a native form that is expressed directly from recombinant cells without any purification or modification steps. A native form of an antigen should provide all the natural epitopes that greatly assist in the selection of neutralizing antibodies. The high density of antigens on VLPs improves the signal / noise ratio for detecting cells that display antigen-specific antibodies on the cell surface and greatly facilitates this sorting step. The recombinant VLP can be generated with the expression of different fluorescent proteins, such as MA-CFP or MA-YFP. Using multiplexed VLPs with different antigens and different fluorescent proteins, cells exhibiting high affinity conjugates (binders), cross-reactive conjugates, or homolog-specific conjugates can be selected. The cells exhibiting high-affinity conjugates can be selected by cells with a relatively high affinity matrix (affinity matrix = ratio of binding activity to low density antigen VLP to high density antigen VLP). Cells that exhibit cross-reactive conjugates for heterologous or different antigens (against the isolation of 2-in-1 or bispecific antibodies) can be selected by binding to cells of different types of VLPs at the same time. Cells expressing homolog-specific conjugates can also be selected by cells that bind to specific antigens but not their homologs.

B cells are thus sorted (eg, using FACS) to provide a single, sorted B cell population. Typically, the B cell lines are sorted into the wells of a standard plate (e.g., a standard 96-well or 364-well plate) such that each single cell line is in a separate well and is not mixed with other cells. It is possible that there is a minimum number of holes (for example, less than 5%, less than 3%, less than 2% or less than 1%, or an undetectable degree) without or having more than one (for example, two) cells, and This does not prevent the overall utility of the screening method (and is not considered part of the desired library). Preferably, each hole in the disk contains a single B cell. Optionally, it is possible that the cells are cultured directly before and / or after the cell sorting step, but the inventors have found that this is different from the technique in the art as necessary. Therefore, by avoiding this step, the method of the present invention assists itself in further streamlining and high throughput.

Next, in the example shown in FIG. 1, the POI-encoded nucleic acid line is enlarged. In this example, this was performed by reverse transcription of the mRNA in the cells of the sorted cell population (meaning that the POI-encoded mRNA was converted to the corresponding POI-encoded cDNA), and this was amplified by PCR. Standard RT-PCR can be used as familiar to those skilled in the art (see, for example, Dixon AK et al., "Trends Pharmacol. Sci., 2000, 21 (2): 65-70"). This produces a DNA library encoding a library of variable regions of antibodies. In this example, the sequences of both V _H and V _L are copied and amplified for each sorted cell line. Those skilled in the art will know that each cell exhibits a single type of antibody binding site. Therefore, each single sorted cell has only a single type of amplified V _H sequence and a single type of V _L sequence. Zoom in (thus, where holes are used, each hole only obtains a single V _H and V _L type, which thus preserves the grouping of the V _H and V _L sequences that form the binding site).

POI coding sequences are also modified at a later stage of the method to generate a library of expression cassettes for expression of POI from host cells. The expression cassette contains a POI-encoding nucleotide sequence and one or more regulatory elements (eg, a promoter and / or enhancer and / or polyadenylic acid) for expression. In one embodiment, the amplification and modification steps can be performed simultaneously using PCR and appropriate templates and primers that will be apparent to those skilled in the art. In another embodiment, amplification and modification are performed in separate steps, for example, amplification and modification. In the example of Figure 1, RT-PCR is performed first, and then the amplified POI coding sequence is modified to generate a performance cassette, each of which contains (in the 5 'to 3' direction): promoter-POI Nucleotide sequence-polyadenylic acid. In this example, a pinch-off transposer element is also added. The transposon element can be a repeat element at the inverted end of the piggyBac (PB) transposon to form a transposon nucleic acid, which contains the following structure: [5 'PB element]-[promoter]-[POI nucleotide sequence]-[ Polyadenylic acid]-[3 'PB element]. In one example, each performance cassette is provided by a linear DNA containing or consisting of the transposon.

PB 5 'end element:

PB 3 'end element:

As shown in the example of FIG. 1, bridge PCR (see, for example, "Biotechniques, 1999, 26 (6): 1082-1086" by Mehta RK and Sihgh J.) can be used to add transposable subelements Construct the transposon.

At this stage of the method, a performance cassette library has been obtained that encodes a library of POI-encoding nucleotide sequences derived from the input cell population. In this example, the scale-up and modification procedure is performed on the single cells sorted into holes in one or more plates. Thus, the result is a sorted library of performance cassettes (in this case, each single hole containing several types of _VH performance cassettes derived from a type of antibody binding site of a single input cell) and a type V _L expression cassette). This sorted performance cassette (in this example, contained in individual transposons, and optionally with linear DNA) is then transfected into the host cell to generate the sorted performance markers once the POI library is sorted Select the host cell bank. In this example, this can be performed by transfecting a performance cassette from a hole in a plate (or set of plates) to a cell with several cells containing the host cell (e.g., a consistent type of cell of the same cell line , Such as CHO or HEK293 or yeast cells). In this embodiment, the sorted cartridge library may use a multi-channel pipette (e.g., one of the techniques known in the art 4, 8, 12, 16 (2 × 8), 64 (8 × 8), 96 (12 × 8), 384, or 1536 channel pipettes) manually or with a robotic arm to simultaneously retrieve the cassette from a hole in the first plate (sorted VH / VL cassette pairs) and transferred to corresponding holes on the second plate, where these holes contain the host cells. By doing so, the relative position and sorted nature of the performance cassette is maintained when transfected into host cells. This has the advantage of maintaining the V _H / V _L cassette sequence pairs linked and not mixed (meaning that each hole in the second plate contains only the host cell and V _H derived from a single input B cell and V _L sequences). Advantageously, if there are also some cassette samples left on the first disc, one can easily identify the source of one or more holes as a useful POI coding sequence (and expression cassette and transposer) by following After screening the second plate for a desired antibody binding site characteristic, reference is made to the desired positive group found on the second plate. Also, advantageously one can provide the host cell in a medium that is desirably supporting the function and maintenance of the host cell (typically different from the environment used in the first plate of cells for sequence amplification and modification). In an alternative embodiment, the host cell line is added to a hole in the disk containing the performance cassette library, so that the sorted arrangement is retained (but this then does not provide the additional advantage of another embodiment, where the latter Performance cassette master disks are retained without host cell mixtures-for example, useful for performing a second transplantation to another disk with a different type of host cell, such as when one wants to evaluate a different host cell type POI performance and display / secretion performance).

An example of an automated multichannel pipette is the Thermo Scientific Matrix Hydra II 96-channel automatic liquid dispenser. V & P Scientific VP 177AD-1 and VP 179BJD are respectively distribution manifolds designed for rapid filling of 96 and 384-well disks, and either of them can be used in the method of the present invention to transfer cassettes to host cells or use For general sample processing.

The output of the method of the present invention is, therefore, in its broadest level, a production of a host cell bank that expresses a POI bank. As discussed above, this can then be used in subsequent screening steps (e.g., using a cell-binding assay, ELISA, surface plasmon resonance, or other test that is applicable to the specific nature of the POI) to identify One or more host cells that exhibit POI with desired characteristics. One can then isolate the POI from the cell or surrounding medium, and / or isolate (and optionally replicate or amplify) a nucleotide sequence (eg, a DNA sequence) encoding the desired POI. The nucleotide sequence can be determined. Such isolated cells can be cultured to produce POI-encoded cell lines (especially useful when the cassette has been stably incorporated into the cell's genome, as it may be incorporated by site-directed genes, for example, using transfection Seat execution). The POI-encoding nucleotide sequence can be inserted into a different expression vector and / or mutation (eg, affinity maturation), or fused to another protein sequence.

Transposon incorporation is achieved by providing a corresponding transposase enzyme in the host cell (e.g., by co-transfecting a performance cassette with a vector containing a transposable gene, or by providing Host cells with such transposase genes (eg, inducible). In one example, each cassette contains a PiggyBac transposable element, and the method uses a piggyBac transposase (eg, wild-type or highly active piggyBac transposase; see, for example, Yusa, K, et al., "PNAS USA , 2011, 10 (4): 1531-1536; and Yusa K et al. In "A hyperactive piggyBac transposase for mammalian applications", PNAS USA, 2010, 108 (4): 1531-1536).

WT PBase:

Highly active PBase:

When a transposon line is used in the host cell for cassette incorporation, it has additional benefits. First, transposons can be incorporated in several copies in a host cell, providing a multi-copy performance cassette to support high-volume POI performance. This can be further enhanced using a highly active transposase enzyme. In addition, transposons can preferably be incorporated at the transcriptional active site, which is also conducive to high-volume and effective POI performance, as demonstrated by mapping analysis of the incorporated sites. This can be seen with piggyBac, for example (see Wang W. et al. In "Chromosomal transposition of PiggyBac in mouse embryonic stem cells", 2008, PNAS USA, 105 (27): 9290-9295; Galvan DL et al. In "Genome-wide mapping of PiggyBac transposon integration in primary human T cells", J. Immunother., 2009, 32 (8): 837-844; and Yang W. et al. In "Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data ", 2009, BMC genomics, 10 (Suppl 3): S7).

Therefore, the present invention provides the following concepts:-

Claims 1. A method of producing a cell encoding a library of proteins of interest (POI), the method comprising:-a) providing a population of cells expressing a POI library; b) sorting the cell population to produce a single cell population that is sorted Each cell contains a nucleic acid encoding a different POI; c) amplifying the nucleic acids contained in the sorted single cell population to produce a sorted amplified nucleic acid library encoding one of the POIs; d) modifying the originating step ( c) the sorted amplified POI-encoding nucleic acids to generate a sorted performance cassette library, each cassette containing a nucleotide sequence encoding a POI and one or more regulatory elements used to express the POI; And e) Transplanting a POI expression cassette from the cassette library to a sorted host cell population, while maintaining the POI performance cassette sorting, and generating a sorted host cell bank expressing the sorted POI library.

Steps (c) and (d) may be performed separately (in any order, for example, (c) then (d)), or performed simultaneously.

Optionally, step (c) includes PCR to amplify the POI coding sequence, for example, RT-PCR using POI-encoded mRNA as a template (eg, one, two, three, or more primers comprising or selected from a sequence identification number: 1 A sequence of -53 of this group, as discussed further below). Optionally, the amplified nucleic acid library is DNA in step (c). In one example, each POI line is an antibody variable domain, and step (c) includes using one or more V region-specific 5 'end primers and / or one or more C region 3' end primers (e.g., Cγ (Eg, mouse Cγ primer) PCR amplifies the POI coding sequence. Optionally, the PCR comprises the 5 'end and / or the 3' end of the POI-encoding nucleotide sequence-RACE. In one example, the 5'-RACE is performed using one or more 5'-end primers, each of which is homologous to the 5'-end UTR or promoter sequence of an antibody variable region. In one example, the 3′-RACE is performed using one or more 3′-end primers, each of which is homologous to an antibody constant region, such as a CH1 or Fc sequence. In this example, each amplified POI coding sequence encodes an antibody chain comprising an antibody variable domain and a constant region. In one example, the 3'-RACE uses one or more human constant region sequences as primers; this then generates a humanized variable region sequence in which each variable region is fused to a human constant region (e.g., a human γCH1 or Fc (such as γ Fc)), thereby providing a human antibody chain (POI) in subsequent performance. This humanization is useful during step (c) because the POIs identified from the post-screening represent human chains that can be used to produce antibody treatments against humans. In one example, the 5'-RACE uses a 5 'end template containing a variable region promoter for generating an amplified nucleic acid comprising (in the 5' to 3 'direction): promoter and coding The nucleotide sequence of POI. Additionally or alternatively, the 3 'end-RACE is used, wherein the RACE uses a 3' end template containing a polyadenylic acid sequence for generating an amplified nucleic acid comprising (in the 5 'end to the 3' end direction ): A nucleotide sequence encoding POI and polyadenylic acid. In this case, enlargement and modification to produce a performance cassette can be performed simultaneously (that is, steps (c) and (d) are performed simultaneously).

In one example, the modification of step (d) is performed using PCR, for example, bridge PCR. For example, step (d) is performed after step (c), such as after RT-PCR or RACE amplification. In this case, the bridge PCR is performed in a step comprising: hybridizing a first primer to the 5 'end of the nucleic acid product in step (c); and hybridizing a second primer to step (c) the nucleic acid product. 3 'end (or to the 3' end of the nucleic acid product of the hybridization step using the first primer). Alternatively, the second primer may be originally used (to hybridize to the product of step (c)), and the product of the second primer may be hybridized to the first primer. Alternatively, the first and second primers and the product of step (c) may be mixed together and subjected to PCR.

In any case, the result is an extended product that contains (in the 5 'to 3' end sequence): [5 'end sequence of the first primer]-[promoter]-[encodes a POI Nucleotide sequence]-[polyadenylic acid]-[3 'end sequence of the second primer]

In one embodiment, the promoter and the polyadenylation system are combined with the POI-encoding nucleotide sequence by step (c), as described above (e.g., with appropriate primers, the 5 'end is used-and 3'-RACE). In another embodiment, the first primer used in step (d) comprises a promoter sequence (for example, the sequence is at the 3 'end of the primer). The result of step (d) is then combined with the promoter and the POI-encoding nucleotide sequence. Additionally or alternatively, the second primer used in step (d) comprises a polyadenylic acid sequence (for example, the sequence is at the 5 'end of the primer). The result of step (d) then combines the polyadenylic acid with the POI-encoding nucleotide sequence. Other combinations are possible, for example, the promoter is added in step (c) using an appropriate primer, and the polyadenylation is added in step (d) using an appropriate second primer. In one example, step (c) (e.g., RACE) adds 5 'and / or 3' sequences to the product nucleic acid, which can be used to hybridize with the primers in step (d), wherein the latter uses bridge PCR .

The result of steps (c) and (d) is always a performance cassette library for representing a POI library. In one example, one or more regulatory elements required or desired for performance (or best performance) are omitted from each cassette, but instead are provided by the host cell genome once the cassette has been Introduced into the host cell.

In one embodiment, step (d) adds individual pinching sequences to the 5 'and 3 "ends of the promoter and the polyadenylate incorporation sequence. For example, the 5' end sequence is a 5 'end transposon Element (eg, a 5 'end PB terminal element), and the 3' end sequence is a 3 'end transposable element (eg, a 3' end PB terminal element, which is relative to the 5 'end element at Inverted). For example, the 5 'end incorporation sequence is provided at the 5' end of the first bridge PCR primer, and / or the 3 'end incorporation sequence is at the second bridge PCR. The 3 'end of the primer is provided. The result is a library of expression cassettes. Each terminal (5' and 3 'ends) is in a transposon element, which means that each cassette is modified to form a transposon. Optional Ground, each performance cassette is generated from a linear DNA that terminates at a 5 'and 3' end (e.g., a transposable element, e.g., terminates in an inverted PB transposable element) of an incorporated sequence. Instead Incorporation sequences can be used in place of transposable elements (see further below); for example, the incorporation sequence can be a homology arm (e.g., at least 15, 20, 50, or 100 consecutive nucleotides), using One or more specific target sites (hybrids with homologous arms) are homologously incorporated into the genome of the recipient host cell. Alternatively, the incorporated sequence may be a site-specific recombination sequence (e.g., lox , Rox, or frt) for site-specific incorporation into the host cell genome with corresponding site-specific recombination sites in one or more desired incorporation sites in the genome (according to the individual Incorporation of the provision or performance of an enzyme (ie, cre, dre, or flp individually). In one embodiment, RMCE uses two incompatible recombination sites for insertion (eg, wild-type loxP and mutant lox, such as lox2272 or lox511).

In one embodiment, one or more regulatory elements (e.g., promoter and / or enhancer and / or polyadenylation and / or a signal sequence) for POI performance are added by step (c) , Such as using RACE. Additionally or alternatively, one or more regulatory elements (e.g., promoters and / or enhancers and / or polyadenylation and / or a signal sequence) for POI expression are added via step (d), such as Use bridge PCR.

Additionally or alternatively, in one embodiment, a 5 'and / or 3' end incorporation sequence is added via step (c), such as using RACE. Additionally or alternatively, a 5 'and / or 3' end incorporation sequence is added by step (d), for example using bridge PCR.

In one embodiment, one or more regulatory elements for POI performance (eg, promoters and / or enhancers and / or polyadenylation and / or a signal sequence), and a 5 'and / or 3 The 'end incorporation sequence is added by step (c), for example using RACE.

In one embodiment, one or more regulatory elements for POI performance (eg, promoters and / or enhancers and / or polyadenylation and / or a signal sequence), and a 5 'and / or The 3 'end incorporation sequence is added by step (d), for example using bridge PCR.

2. The method of concept 1, wherein the sorted performance cassette is transfected into the sorted host cells in step (e).

The batch transfer according to this embodiment of the present invention is superior to the prior art method of using molecular colonization to transduce a POI-encoding nucleotide sequence into a host cell. As explained above, the latter requires laborious and time-consuming sequencing, analysis, and sub-breeding of individual POIs that have been modified by including terminal restriction sites to enable introduction into host cells in subsequent steps Coding sequence. Typically, once the correct PCR POI coding sequence with restriction sites has been identified, this is then selected as an individual sequence to facilitate introduction into the host cell, which is then grown to produce the selected POI Sequence of a population of cells. This multi-step, laborious molecular selection process is performed for each POI variant in the pool included in the subsequent screening. Therefore, prior art screening methods can take weeks (typically in the 6-8 week hierarchy) to perform a useful starting cell bank, such as antibody-producing cells. In contrast, the method of the present invention, which uses the sorting batch to transfer the entire performance cassette of the POI (that is, including the POI and the regulatory elements for performance), provides a very fast method for generating a sorted POI library for screening. Technology. This makes the method suitable for high-throughput automation of screening. For example, the inventors-performing the manual operation of the method-using a 4 × 96 well plate (nearly 186 input B cells), have been able to perform the production of a sorted host cell for POI performance in only 2 days Library. Screening of this performing POI library can be performed manually in about 2 days. Obviously, automation accelerates this more (and advantageously minimizes cross-contamination between sorted aliquots).

For batch transfer performance cassettes, several sorted performance cassettes are mixed in the same operation (e.g., a single cassette aspiration and delivery step, meaning a single pipetting step) with host cells for transfer Into cells (for example, by subsequent or simultaneous transfection into cells). This operation is, for example, a single transfer by a pipette (for example, using a multi-channel pipette, such as a 4, 8, 12, 16, 64, 96, 384, or 1536 in a single operation Channel pipette). In one example, at least 4 sorted performance cassette aliquots are mixed with sorted host cells in a single operation such that each performance cassette aliquot is a single cell aliquot Mix (for example, in a separate container, for example, in a hole in a tray or in a test tube in a tube rack). In an example, at least 4, 8, 12, 16, 24, 32, 40, 48, 56, 64, 96, 384, or 1535 aliquots of sorted performance cartridges are processed in the same operation as Host cells are selected such that each performance cassette aliquot is mixed with an individual cell aliquot (for example, in a separate container, for example, in a well in a plate or in a tube rack). Test tube). In one embodiment, the operation is a manual operation (for example, by using a multi-channel pipette). In another embodiment, the operation is automatic, for example, by an automatic liquid dispensing device (for example, a liquid handling robotic arm)

Advantageously, the inventors have discovered that it is possible to batch transfer the performance cassette derived from step (d) to the sorted host cell without purifying the cassettes, but still in step (e) A useful host cell bank is produced. This provides higher processing speed and throughput, and makes the method suitable for simpler automation.

3. The method as in concept 1 or 2, wherein (i) the sorted performance cassette produced in step (d) is provided in a number of containers that are fixed relative to each other (e.g., on a tray Holes or test tubes in a tube rack), wherein each container contains a separate type of performance cassette such that the relative position of the performance cassettes relative to each other is predetermined; and (ii) the performance cassettes are in steps (e) Transplantation into the sorted host cells such that the relative positions of the performance cassettes are maintained.

In one example, each container contains a cassette encoding a first type of POI derived from an individual single cell provided in step (a), and a cassette encoding a second type of POI derived from the single cell By. For example, each of the containers containing a cassette encoding a single cell derived from the V _H and V _L sequences. In this manner, the variable domains that make up the individual binding sites of input cells (where these encode antibody binding sites, such as plasmablasts or plasma cells) are held together in the sorted library, but Not mixed with sequences derived from another cell. This sorting is thus advantageously maintained in later steps of the method and is traceable in subsequent screening results.

4. A method as in any of the preceding concepts, wherein (i) the performance cassette produced by step (d) is sorted by providing several containers (e.g., holes in a tray or in a tube rack) Test tube), wherein each container contains the POI coding sequence of the single cell sorted in step (b); (ii) the sorted host cell line of step (e) is provided in several containers (e.g., , Or a test tube in a hole in a plate or tube rack), and (iii) the performance cassettes are transfected into the sorted host cells in step (e) such that the host in each individual container The cells are only mixed with POI coding sequences derived from the single cells sorted in step (b).

5. The method of concept 3 or 4, wherein the sorted performance cassette in step (d) is provided in a plurality of containers which are fixed relative to each other (for example, a plurality of containers having an X container multiplied by One of the arrays of the Y container, such as an 8 × 12-well plate (96-well plate) or a plate having multiples of the 8 × 12-well arrangement (for example, a 384-well plate)); The host cell line is provided in several containers that are fixed relative to each other and contain the same arrangement as the container used in step (d) (e.g., in steps (d) and (e) Both of these libraries are provided on 96-well or 384-well plates of the same or essentially the same dimensions), so that the sorting system is maintained in step (e).

6. A method as in any of the foregoing concepts, wherein the sorted host cell bank line is capable of stably expressing the POI bank.

Alternatively, the sorted host cell bank can perform transiently. Stable performance (e.g., as a result of gene incorporation into the host cell's genome as a cassette) is beneficial for long-term supply of cells that have been identified after screening-and the POI that they exhibited-and also for cells waiting to be screened (If the host cell produced in step (e) is stored for a period of time before being used for screening).

7. A method as in any one of the preceding concepts, wherein the sorted POI expression host cell bank produced in step (e) is provided in several containers (e.g., test tubes or wells), wherein each container contains the (b) POI of single cells sorted in.

Such test tubes can be fixed in a tube rack or stand; such holes may be fixed by being provided on one or more trays.

8. The method of concept 7, wherein each host cell exhibits a first and a second POI, wherein the POIs are different, such as a subunit of a protein, such as the binding site of an antibody or a T-cell receptor. Change domain.

9. A method as in any of the foregoing concepts, wherein step (b) comprises sorting a single cell into individual containers (e.g., individual holes in one or more plates) and performing step (c) in those containers ) And (d) while maintaining sorting.

10. A method as in any of the foregoing concepts, further comprising screening the sorted POI library to identify a POI with a desired characteristic (eg, binding to an antigen or antibody; or binding affinity to a cognate ligand or antigen ) And / or a nucleotide sequence (eg, DNA or RNA, such as mRNA or cDNA) encoding the identified POI.

11. The method of concept 10, further comprising identifying, amplifying, or synthesizing a nucleotide sequence encoding the identified POI (e.g., using PCR or by culturing a selected host cell or a derivative thereof); and optionally The identified, amplified or synthesized nucleotide sequence is used to make an isolated POI.

12. A method as in any of the foregoing concepts, further comprising screening the sorted POI library to identify a POI having a desired characteristic (eg, binding to an antigen or antibody; or binding affinity to a cognate ligand or antigen) And isolate a host cell expressing the identified POI; and optionally subculturing the cell to produce a cell line expressing the POI.

13. A method as in any of the foregoing concepts, wherein step (e) comprises gene incorporation (eg, chromosomal incorporation) into a POI expression cassette into the genome of an individual host cell for expressing the individual POI. Alternatively, one or more of these cassettes are provided episomally in their individual host cells for transient POI performance.

14. The method of concept 13, wherein the gene incorporation is performed using a predetermined genomic nucleotide sequence motif for inserting the expression cassette into the genome of an individual cell.

For example, the motif is a nucleotide sequence used by a transposon for incorporation (such as the TTAA motif used by a PB); or a nucleotide sequence that can be combined with a cassette by homologous recombination 5 'and 3' ends incorporate sequence recombiners; or motifs that incorporate a site-specific recombination site are used.

15. The method of concept 14 wherein each cell genome contains more than one copy of the sequence motif.

16. The method according to idea 13, 14 or 15, wherein the gene incorporation is performed by transposon-mediated incorporation.

Transposable elements suitable for use as cassette 5 'and 3' incorporation sequences are type II transposable elements (e.g. piggyBac transposable inverted repeat elements or Mariner transposable elements), or Sleeping Beauty transposable elements or Tc1 Class element (TLE).

17. The method of any one of concepts 13 to 16, wherein step (e) comprises multiple insertion of a performance cassette into the genome of an individual host cell.

Each cassette is optionally provided as part of a linear nucleic acid, such as a linear DNA. For example, each cassette is a linear transposer, which contains or consists of 5'- and 3'-terminal transposable elements (such as the piggyBac inverted end repeat element), which accompanies the transposable elements. POI nucleotide sequence and regulatory elements for expression (etc.). In one embodiment, it is further sequenced at the 5 'end of the 5' end transposable element and / or at the 3 'end of the 3' end transposable element; in another embodiment, these elements are individually At the 5 'and 3' ends of the cassette.

18. A method as in any of the foregoing concepts, wherein the host cell line is a cell of a mammalian cell line (e.g., CHO or HEK293 cells) or a yeast cell.

For example, where each host cell line is a mammal (e.g., human or non-human animal, plant or insect or rodent or mouse or rat or rabbit or chicken or camelid (Camelid) or fish cell), bacteria Or yeast cells.

19. A method as in any of the foregoing concepts, wherein in step (a) the cell line is a cell isolated from one or more animals.

Optionally, each cell line of step (a) is a mammal (e.g. a human or non-human animal, plant or insect or rodent or mouse or rat or rabbit or chicken or camel or fish cell), a bacterium Or yeast cells.

Optionally, all cell lines of step (a) are cells of the same type of tissue or compartment of an organism (etc.). For example, they are all liver, kidney, heart, brain, blood, lymphoid, prostate, ovary or germ cells of one or more organisms, such as human patients or non-human animals or rodents or mice or mice Rat or rabbit, chicken or camel or fish.

20. The method according to any one of the preceding concepts, wherein in step (a) the cell comprises or consists of a B cell, a germ center cell, a memory B cell, an antibody secreting cell, a plasma cell, or a plasmablast.

21. A method as in any of the foregoing concepts, wherein each POI is an immunoglobulin (e.g., an antibody or T cell receptor) chain or a portion thereof (e.g., a variable domain).

22. The concept of a method according to any of the foregoing, wherein each POI comprises or consists of an antibody variable domains (e.g., V _H, V _HH domains or V _L dAb or or Nanobody ^TM).

23. A method as in any of the preceding concepts, wherein each cell of step (a) exhibits a first and a second POI, wherein the POIs are different from each other; wherein step (b) includes sorting a single cell into individual containers (E.g., individual holes in one or more plates), and performing steps (c) and (d) in the containers, where after step (c), each container contains The amplified first POI is a mixed amplified first POI; and wherein step (e) comprises mixing individual first and second POI-encoding nucleic acids derived from a different container with a host cell; wherein the derived from step (a) is the same The first and second POI cells of the cell are transfected to the same host cell for expression of the first and second POI by the host cell, thereby generating a sorted host cell bank, each of which collectively represents an individual first And the second POI.

24. The method of concept 23, wherein the first and second POI lines derived from the same cell are homopolypeptides, and the two together form a functional protein (eg, V _H and V forming an antigen binding site) _L domain).

25. The method of concept 24, wherein the first and second POI individually or comprises an antibody V _H and V _L domains, e.g., the first and second lines individually POI is an antibody with heavy and light Group chain.

26. A method as in any of the foregoing concepts, wherein step (b) comprises binding the POI expressed by the cell to a cognate ligand (eg, binding the antibody binding site expressed by the cell to an antigen of interest); optionally Wherein the ligand binds to the POI expressed on the surface of the cell; and further sorts and isolates cells whose POI appears to bind the ligand, thereby generating the sorted cell population.

27. The method of concept 26, wherein the FACS cell sorting line is used; optionally fluorescent FACS.

28. The method of concept 26 or 27, wherein each sorted cell of step (b) is provided in a separate container (e.g., a hole on a plate) such that each such container (e.g., a hole) contains No more than one cell type.

29. The method of concept 28, wherein the sorted cell population is provided in a hole on one or more disks, said disks containing a total of less than 5, 4, 3, 2, 1 or 0.5% of holes Contains more than one type of cells, and / or less than 5, 4, 3, 2, 1 or 0.5% of the pores are free of cells.

30. A method as in any of the foregoing concepts, wherein step (c) is performed using PCR, for example, RT-PCR using POI-encoding RNA (e.g., mRNA).

31. A method as in any of the foregoing concepts, wherein step (d) is performed using PCR, such as bridge PCR.

32. A method according to any one of the preceding concepts, wherein step (d) comprises modifying the amplified nucleic acid by combining with a predetermined sequence such that the predetermined sequence sandwiches 5 'and / Or 3 'end; optionally wherein the modification places a regulatory element (eg, a 5' end promoter and / or a 3 'end polyadenylation) and / or a transposer element (eg, a piggyBac transposer element ) Squeeze the 5 'and / or 3' end of the POI-encoding nucleotide sequence.

33. The method of concept 32, wherein each POI comprises an antibody variable domain, and step (c) or (d) combines the POI-encoding nucleotide sequence with an antibody constant region (optionally a human constant region, or A species different from the species of the C region contained in the POI in the cell of step (a)) to generate a nucleotide sequence encoding an antibody chain (optionally a humanized chain).

For example, the cell of step (a) encodes a POI that contains a constant region of a non-human vertebrate (e.g., a rodent such as a mouse or rat), and these are derived from humans by step (c) or (d) The constant region is replaced. For example, these POIs are antibody chains (e.g., heavy chains) that include a human variable domain and a rodent (e.g., mouse or rat) constant region that is humanized by the methods of the present invention. This line is convenient because it provides a high-throughput method to humanize antibody chains and antibodies on a large scale, and enables subsequent selection, production, and development of cells and expression vectors in the context of the final human antibody / chain format. For human medical drug use. The prior art does not do this.

34. The method of concept 33, further comprising screening the sorted POI library to identify host cells (e.g., specific antigen-binding or antigen-binding affinity) exhibiting an antibody chain having a desired characteristic, and identifying the host cells The antibody chain encoding nucleotide sequence, using the antibody chain encoding nucleotide sequence to generate a copy of the recognized antibody chain, and formulating the copy as a pharmaceutical composition (optionally further with one or more drugs, excipients , Diluent, or vehicle combination) for human medical treatment; and optionally administering the composition to a human patient for medical treatment of the patient.

35. A method as in any of the preceding concepts, wherein step (e) is automated; optionally, wherein one or all of steps (b) to (c) are also automated.

Automation may include controlling the process by a computer programmed to implement any method, aspect, configuration, embodiment or example of the invention.

36. A method as in any one of the preceding concepts, wherein (i) steps (b) to (e) are performed in an equivalent of at least 180 cells (if step (a) is performed for no more than 1 or 2 days); and / Or (ii) The expressed POI library is screened for a desired characteristic, and one or more corresponding host cells or POI-encoding nucleotide sequences are identified in no more than 4 days.

The present inventors used nearly 400 input B cells and screened for antigen-specific antibodies, with (a) taking 2 days, and (b) taking 3 days to implement-all manually. Obviously, this would be faster if automation were used. Therefore, the present invention provides significant time savings over prior art techniques, which typically takes 6-8 weeks to perform such screening.

37. An automated device for performing a method according to any one of the preceding concepts, the device comprising a. For holding in several containers (e.g., holes in one or more trays, or in a tube rack or rack Test tube, as described above), a tool for sorting a single cell population, wherein each single cell line is in a separate container, each cell contains a nucleic acid encoding an individual POI; b. Used to deliver PCR reagents to the container A tool for amplifying nucleic acids contained in the sorted single cell population to generate a sorted amplified nucleic acid library encoding a POI; c. A tool for delivering reagents to a container for modifying the sorted Amplified POI-encoding nucleic acids to generate a sorted performance cassette library, each cassette containing a nucleotide sequence encoding a POI and one or more regulatory elements used to express the POI; d. There are tools for sorting host cell populations in several containers; e. For transplanting (optionally batch) POI performance cassettes from the cassette library to sorting in the containers A host cell population tool while maintaining the POI performance cassette sorting; f. means for performing introduction (eg, transfection) of a performance cassette into host cells within a container to generate a sorted host cell bank expressing a sorted POI library; and g. optionally, a program to A computer implementing the method of any aspect, configuration, embodiment or example of the invention.

38. The apparatus of concept 37, further comprising a means for sorting a cell population (e.g., a tool for performing FACS) to generate the sorted single cell population

39. The device of concept 37 or 38, further comprising means for controlling the operation of the device, for automatically performing the method of any one of concepts 1 to 36.

40. A kit for carrying out the method of any one of concepts 1 to 36, the kit comprising a device such as one of concepts 37, 38 or 39, together with a transposable element containing the method for performing concept 32 (etc. ) Nucleic acid.

The transposon element can be implemented by, for example, linear DNA. In one example, the elements are a transposable element (eg, a class II transposer) that mediates DNA incorporation through a splicing and sticking translocation mechanism. In one example, the elements are PB or Mariner-type elements or Tc-1 type elements (TLE).

41. An expression cassette for expressing a POI in a host cell, the cassette being provided by a linear nucleic acid (e.g., linear DNA) comprising a transposon comprising the 5'- and 3'-ends A transposon element, a POI-encoding nucleotide sequence accompanying the transposon elements and regulatory elements (etc.) for the performance of the POI.

Such cassettes are useful for gene incorporation of expressible POI sequences into host cells, such as for producing cell lines to provide a source of POI, and / or for use in the screening methods of the present invention. The transposable elements may be any such elements disclosed herein.

In one example, the cassette contains or consists of a transposon, the transposon contains 5'- and 3'-terminal transposable elements (such as the piggyBac inverted end repeat element), which accompanies the transposable elements One of the POI-encoding nucleotide sequences and one or more regulatory elements for expression (etc.). In one embodiment, the cassette further comprises a sequence at the 5 'end of the 5' end transposable element and / or at the 3 'end of the 3' end transposable element. In one example, the cassette contains an additional nucleotide sequence corresponding to a nucleotide sequence of the host cell genome, and the additional sequence is at the 5 'and / or 3' end of the POI-encoding nucleotide sequence. . For example, the additional sequence corresponds to a genomic host cell sequence that is actively transcribed in the host. Therefore, the POI coding sequence is inserted into the host in an environment suitable for the active transcription of the POI sequence.

In one example, as used herein, a "population" (eg, a cell or cassette population) or "library" includes at least 10, 100, 1000, 104, 105, or 106 members.

42. A performance cassette group as in concept 41, wherein the group codes a POI library.

43. A sorted group of performance cassettes as concept 42.

44. A sorted performance cassette family encoding a POI library corresponding to a POI represented by a cell population, each cassette containing a nucleotide sequence encoding a member of the POI library, and a Or multiple regulatory elements for POI expression (when in a host cell), wherein each of the cassettes contains the arrangement (in the 5 'to 3' direction): the transposon element-[POI nucleoside Acid sequences & regulatory elements (etc.)]-transposable elements, and expression cassettes used to express POI corresponding to the POI of different cells are separated from each other in the sorted population (e.g., different holes in a plate (For example, one cassette species per hole in one or more disks).

In one example, each cassette is capable of expressing (derived from) a single cell POI, such as an antibody heavy or light chain or fragment thereof derived from a single B cell.

In one example, the piggyBac element is used.

45. The group of idea 44, wherein each performance cassette is provided by a linear DNA.

46. The cassette population of any one of concepts 42 to 45, wherein each cassette is in a host cell.

47. A sorted host cell population comprising a sorted performance cassette family as in any of concepts 43, 44 and 45 for expressing the sorted POI library.

48. A method of making a transposon comprising a nucleotide sequence of interest (NOI), the method comprising a. Providing a first nucleotide sequence (e.g., provided by DNA or RNA) comprising (at the 5 'end To the 3 'end direction) A, B and C (optionally composed of the 5'-ABC-3' structure), where A is a first homologous sequence and B is a sequence containing the NOI (or NOI) nucleotide sequence, and C is a second homologous sequence; b. Provide a first template nucleotide sequence comprising (in the 5 'to 3' direction) W and X (or by The two are composed), wherein W is a nucleotide sequence including (or consisting of) a first transposer element (such as a piggyBac terminal repeat element), and X is a third homologous sequence; and c Provide a second template nucleotide sequence comprising (in the direction of 5 'to 3') Y and Z (or consisting of both), wherein Y is a fourth homologous sequence, and Z is A nucleotide sequence comprising (or consisting of) a second transposer element (such as a piggyBac terminal repeat element); and any one of the following d. (I) the first nucleotide sequence and the first template Mixed to hybridize the first and third homology arms Nucleic acid amplification and extension (e.g., using PCR) to extend the first nucleotide sequence using the first template to generate a first extended nucleotide sequence (first ENS), which includes (in 5 'end to 3' end) W, B, and C; and (ii) mixing the first ENS with the second template to hybridize the second and fourth homology arms together and perform nucleic acid amplification and extension, To extend the first ENS to generate a second ENS, which includes (in the direction from the 5 ′ end to the 3 ′ end) W, B, and Z (or consists of the three); or (ii) the first core A nucleotide sequence is mixed with the second template to hybridize the second and fourth homology arms together and perform nucleic acid amplification and extension (eg, using PCR) to extend the first nucleotide sequence using the second template to Generating a third extended nucleotide sequence (third ENS), which includes (in the 5 'to 3' direction) A, B, and Z; and (ii) the third ENS and the first template Mixing to hybridize the first and third homology arms together and perform nucleic acid amplification and extension to extend the third ENS to generate a fourth ENS, which includes (in the 5 'end to the 3' end direction) W , B and Z (or by the three Or (iii) mixing the first nucleotide sequence with the first and second templates to hybridize the first and third homology arms together, and hybridize the second and fourth homology arms Together, and perform nucleic acid amplification and extension (such as using PCR) to use the second template to extend the first nucleotide sequence to generate a fifth ENS, which includes (in the 5 'end to the 3' end direction) W, B, and Z (or consisting of the three); and e. Separating ENS including (in the 5 ′ end to the 3 ′ end) one of W, B, and Z (or consisting of the three), thereby generating An isolated transposon comprises a NOI pinched by a transposon element; and f. Optionally introducing the isolated transposon to a recipient cell such that the transposon is incorporated into the genome of the cell.

Optionally, one, more or all of the homologous sequences comprise at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200 or more contiguous nucleotides Nucleotide sequence.

In one example, the NOI encodes a POI, protein domain, or protein fragment or is itself one or more regulatory elements (etc.). For example, the NOI encodes a POI that is a heterolog or homolog of a protein in the recipient cell genome or in a human or non-human vertebrate.

In one embodiment, W and X are the 5 'and 3' ends of the first template sequence, respectively. Additionally or alternatively, Y and Z are the 5 'and 3' ends of the second template sequence, respectively. When W and X are the 5 'and 3' ends of the first template sequence, and Y and Z are the 5 'and 3' ends of the second template sequence, the product of the method is A linear transposon of a seat element, which is very suitable for gene incorporation to modify host cells.

Optionally the first template consists of 5'-W-X-3 '. In one example, no nucleotide sequence is interposed between W and X. In another embodiment, there is further a nucleotide sequence between W and X, such as a regulatory element or exon or other desired nucleotide sequence (such as a protein coding sequence). The product will become tightly integrated upstream of the NOI. This is useful, for example, for constructing a performance cassette that is used to incorporate a promoter upstream of a NOI (where the NOI encodes a POI) for subsequent performance of the POI, once the transposon has been inserted Into a host cell genome.

Additionally or alternatively, optionally the second template nucleotide sequence consists of 5'-XY-3 ', or there is an intervening nucleotide sequence between X and Y, such as a regulatory element or exon or For other desired nucleotide sequences (such as protein coding sequences), these will become incorporated immediately downstream of the NOI in the product of the method. This is useful, for example, for constructing a performance cassette that is used to incorporate a polyadenylic acid downstream of a NOI (where the NOI encodes a POI) for subsequent performance of the POI. The position has been inserted into the genome of a host cell. In another example, the intervention sequence coding will become a protein fused to the POI, and a fusion product will be generated according to the performance. For example, the POI includes or consists of an antibody variable domain, and the intervention sequence includes or consists of an antibody constant region coding sequence. For example, the intervention sequence encodes an antibody Fc or antibody CH1 or CL domain. In one example, the Fc or constant region or protein encoded by the intervention sequence is a human Fc, constant region or protein. This is useful for humanizing the POI (for example, when the POI is a variable domain, such as a human variable domain, a humanized antibody chain is produced).

49. The method of concept 48, wherein there is an intervention nucleotide sequence between W and X, and / or an intervention nucleotide sequence between Y and Z; optionally wherein the intervention sequence or each intervention The sequence is a regulatory element or protein coding sequence.

50. The method of concept 49, wherein the NOI encodes a protein domain (e.g., an antibody variable domain), and between Y and Z is a constant region encoding an antibody (e.g., antibody Fc, e.g., human Fc) The nucleotide sequence of the transposon product thus encodes a fusion protein comprising a protein domain (eg, encoding an antibody chain) fused to the constant region of an antibody.

51. The method of any one of concepts 48 to 50, wherein one or more of the first and second homology arms are by PCR (e.g., 5 'and / or 3'-RACE) and NOI Combined to form the first nucleotide sequence before performing the extension.

52. A method of making a transposon library, wherein members of the library encode different POIs (eg, different antibody variable domains), the method comprising i. Providing a first nucleotide sequence family comprising a NOI library And ii. For each first nucleotide sequence, the method of any one of concepts 48 to 51 is performed, thereby generating a transposon library encoding a POI library.

53. The method of concept 52, comprising sorting the first nucleotide sequence to provide a sorted population before performing step (ii), where the sorted transposon library line is generated, which encodes a Sorted POI library.

54. The method of concept 52, wherein the transposon lines of the transposon bank are mixed together.

55. The method of any one of concepts 52 to 54, wherein the transposon line of the library is introduced into a recipient cell such that the transposon is incorporated into the genome of the cell, and each incorporated transposon comprises a transposon The element-punched POI expression cassette contains a NOI and one or more regulatory elements for expressing the POI in a host cell.

56. The method of idea 55 when relying on idea 53, wherein the sorting line is maintained when the transposon is introduced into a cell, thereby generating a sorted cell bank expressing a sorted POI bank.

57. A method of producing a host cell for expressing a POI, the method comprising a. Providing at least a first and a second performance cassette, wherein each performance cassette comprises i. A first incorporated element and the first A second incorporated element 3 ′ of the incorporated element nucleotide sequence; and ii. A nucleotide sequence encoding a POI and one or more regulatory elements for expressing the POI between the incorporated elements; iii. The incorporated elements are capable of predetermining a nucleotide sequence motif by recognizing one of a nucleic acid and inserted into the nucleic acid using an incorporated enzyme; b. providing a host cell whose genome contains several such moieties Sequencer; and c. Simultaneously or sequentially introducing the first and second expression cassettes into the host cell, wherein each cassette is based on the motif gene incorporated into the host genome for use by the The host cell exhibits POI; and d. Optionally produces a cell line that exhibits POI in a step comprising culturing the host cell.

This aspect of the invention is useful for generating host cells and cell lines for relatively high performance of one or more POIs of interest. The incorporation of genes into multiple POI cassettes at multiple loci provides stable performance, and it also has the potential to target transcriptionally active regions in the host genome. A sequence motif is used to guide the insertion to a useful site, and as used in the art, it is preferably randomly incorporated into the sequence.

58. The method of concept 57 wherein the first and second incorporated elements of the first cassette are individually consistent with the first and second incorporated elements of the second cassette.

In one example, each cassette contains first and second transposable elements, such as transposable elements of the same type (eg, PB or type II transposers). In one example, all elements are site-specific recombination sites, such as lox sites or frt sites or a mixture of these. In another example, all elements are homology arms (a contiguous nucleotide sequence sufficient for homologous recombination in the host cell). In one example, the site-specific recombination sites are the same, or they are different (e.g., mutually incompatible sites (e.g., loxP and lox511 or 2272) for performing RMCE (recombinase-mediated Cassette exchange) for targeted insertion of cassettes into the genome.

59. The method of concept 57 or 58, wherein the first and second incorporated elements of each of the first and second cassettes are in an inverted orientation (e.g., an inverted PB transposer element or an inverted site) Specific recombination site).

60. The method of any one of concepts 57 to 59, wherein one or more of the motifs are engineered into the chromosome of the host cell prior to performing step (c), such as lox site pair engineering Into one or more host chromosomes, which correspond to the pairs of lox pairs used in the cassette.

61. The method of any one of concepts 57 to 59, wherein one or more of the motifs are endogenous to the host cell genome; optionally, each of the motifs where the cassette is incorporated This is an endogenous motif.

For example, transposons recognize endogenous motifs (eg, TTAA in the PB recognition genome).

62. The method of any one of concepts 57 to 61, wherein at least 3 cassette line genes are incorporated into the host cell genome, such as within one or more host chromosomes-this is useful for stable performance.

63. The method of any one of concepts 57 to 62, wherein the cassette gene incorporation site is active in transcription of the POI coding sequence.

This can be achieved using transposons (eg PB) in the cassette.

64. The method of any one of concepts 57 to 63, wherein each cassette is incorporated by homologous recombination between the incorporation site and the host genome; the incorporation site and the host Site-specific recombination incorporation between genomes; or incorporation mediated by transposons.

65. The method of concept 64, wherein the enzyme is selected from a recombinase or a translocation (for example, an enzyme corresponding to the incorporated element PBase (such as highly active PBase), flp or cre recombinase).

In one example, the host cell has been engineered to express the enzyme (s), such as a gene incorporated from a gene (eg, an inducible gene). In another embodiment, the enzyme is expressed from a free genomic vector. In another example, the enzyme is introduced into the host cell.

66. The method of any one of concepts 57 to 64, wherein each cassette is a transposer.

67. The method of any one of concepts 57 to 66, comprising providing a host cell population and performing the method of any one of concepts 57 to 66 on several host cells of the population; and optionally isolating a step by (c) or (d) the host cell produced.

68. The method of any one of concepts 57 to 67, comprising isolating a host cell produced by step (c) or (d) and identifying, amplifying, or synthesizing a nucleotide sequence encoding a POI that can be expressed by the cell And optionally using the identified, amplified or synthesized nucleotide sequence or a mutation thereof to generate an isolated POI.

69. The method of concept 68, comprising formulating the isolated POI into a drug for use in human medicine; and optionally administering the drug to a human patient.

70. A host cell population obtained by a method according to any one of concepts 57 to 69, each cell containing a number of genes incorporated expression cassette for the expression of POI, each host cell running through its genome Adjacent to an incorporated expression cassette contains several identical nucleotide sequence motifs for representing the POI derived from each such cassette; each incorporated cassette contains a. A first merger The element sequence and a second incorporated element sequence 3 ′ of the first incorporated element nucleotide sequence; and b. A nucleotide sequence encoding one or more POIs between the incorporated element sequences and one or more useful sequences For expressing the regulatory elements of this POI.

71. The host cell of Concept 70, wherein all POI lines expressed by the cell are the same POI.

72. The host cell of concept 70, wherein the cell expresses a first and a second POI (eg, VH and VL domains of a single antibody type; or heavy and light chains of a single antibody type), which are combined together to form A functional protein or ligand (eg, an antigen) binding site.

73. An antibody or antigen-binding site of an antibody for use in human medical treatment, wherein the antibody or binding site has been isolated from a host cell produced by a method such as any one of concepts 57 to 69 Or has been isolated from a host cell population according to any one of concepts 70 to 72.

74. A nucleic acid mixture comprising a first isolated nucleic acid and a second isolated nucleic acid, wherein the first nucleic acid is capable of hybridizing to the 5 'end UTR sequence of the human antibody V region of a gene comprised by a target nucleic acid (Meaning, a nucleotide sequence), wherein the gene encodes a human V region; and the second nucleic acid line is capable of hybridizing to a second sequence, wherein the second sequence is included by the target nucleic acid, and The 3 'end of the UTR sequence, wherein the first isolated nucleic acid comprises a sequence (or consists of the sequence) that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to ( Or 100% consistent with) selected from the group consisting of sequence identification number: 1-47.

Sequence identification number: 1-47 contains a human variable region-specific sequence as shown in Table 1 (more specifically, a human variable region-specific 5 'terminal UTR nucleotide sequence). "Specificity" means that such a sequence can be used as a 5 'end primer sequence in standard PCR (e.g., RT-PCR) of human variable region nucleic acids.

Sequence identification number: 1-17 contains human heavy chain variable region-specific sequences.

Sequence identification number: 18-26 human kappa chain variable region-specific sequences.

Sequence identification number: 27-47 human λ chain variable region-specific sequence.

In one embodiment, the present invention provides a nucleic acid (such as a PCR primer or a vector for homologous recombination), the nucleic acid comprising at least 15 consecutive nucleotides (or Consisting of), used to hybridize to the 5 'end UTR sequence of the gene segment indicated as Y in Table 2, for example, to perform PCR to copy the gene segment, or to hybridize a homologous recombination vector to the 5' A terminal UTR sequence is used to modify the gene segment. In one example, the nucleic acid comprises (or consists of) at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25, or all of the sequence X. In one example, the contiguous nucleotide ends with the 3 'terminal nucleotide of the sequence X (meaning that the continuous nucleotide system extends from the 3' end to the 5 'end of X). In one embodiment, the invention provides a mixture of two or more such nucleic acids, such as for PCR copying two or more variable region sequences (eg, using DNA, cDNA, or RNA derived from corresponding B cells). In one example, two, more or all of the nucleic acids in the mixture copy the VH gene segment. In one example, two, more or all of the nucleic acids in the mixture copy the Vλ gene segment. In one example, two, more or all of the nucleic acids in the mixture copy the Vκ gene segment. Optionally, the nucleic acid or each nucleic acid immediately comprises a promoter nucleotide sequence at the 5 'end of the UTR sequence (or the 15 or more consecutive nucleotide portions). For example, the promoter sequence is one of the following CMV promoter sequences: 5'-CTTACTGGCTTATCGAAATTAATACGACTCAGATC-3 '(sequence identification number: 54)

In one example, the present invention provides: a PCR primer or homologous recombination vector, which comprises at least 15 consecutive nucleotides in the UTR sequence of a human antibody variable gene segment for hybridization to Y indicated in Table 2 The UTR sequence of the 5 'end of the variable gene segment of the antibody, wherein the primer / vector sequence is selected from the group consisting of the sequence shown as X in Table 2.

In one example of the nucleic acid, mixture, or primer of the present invention, in a PCR reaction, each nucleic acid or primer is at a temperature from, for example, 45-70oC (for example, at 50 ° C, or 60 ° C, or 68 ° C), or 60-75 ° C. Hybridize to its homologous sequence at temperature. Those skilled in the art will know the cycle time and temperature to perform the PCR reaction.

Each nucleic acid of the invention and the mixture of the invention are useful for performing PCR amplification or replication of a target nucleotide sequence, wherein the target nucleotide sequence encodes a human antibody variable domain or a protein comprising the domain For example, PCR of human variable region-encoding nucleotide sequences (etc.) isolated from one or more cells (eg, B cells). Therefore, in one embodiment, each nucleic acid line is a PCR primer.

Each nucleic acid of the invention and the mixture of the invention perform homologous recombination to modify a target nucleotide sequence (e.g., a sequence contained in the genome of a cell, such as a mammalian cell, such as an ES cell or CHO cell). ) Is useful. For homologous recombination, as known to those skilled in the art, one uses a nucleic acid vector comprising a 5 'homology arm, a 3' homology arm, and optionally one of the predetermined interest in between. Nucleotide sequence. The sequence may, for example, encode a POI, a protein domain, or contain a regulatory element. In an alternative, there is no intervening sequence between the homologous arms (and in this case, the vector is used to delete sequences from the genome that lie between regions that hybridize with the homology arm, such as mature lines Known by the artist). In this embodiment, the present invention provides a homologous recombination vector, wherein the vector comprises a 5 'end arm, a 3' end homology arm, and optionally a nucleotide sequence therebetween, wherein the 5 'end The arm contains (or consists of) a sequence that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) selected from the sequence identification number: A sequence of the group consisting of 1-47, and / or wherein the 3 'end arm comprises a sequence (or consists of) of which is at least 90, 91, 92, 93, 94, 95, 96, 97 , 98, or 99% agree (or 100% agree) with a sequence selected from the group consisting of sequence identification numbers: 48-53. This makes it possible to use homologous recombination of specific V and / or C gene segments of a gene target Ig locus in a vertebrate.

The present invention, therefore, also provides a method of modifying an Ig locus contained in a vertebrate cell, the method comprising introducing the vector of the invention into a cell (e.g., by transfection) and performing homologous recombination to Modifying the Ig locus; and optionally expressing an antibody V domain or chain from the modified locus. Optionally, the sequence of the V domain is identified or copied or isolated from the cell and used to produce an antibody or a pharmaceutical composition comprising such an antibody for human medical use.

The present invention further provides a PCR primer comprising a sequence (or consisting of) thereof, the sequence being at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) ) A sequence selected from the group consisting of sequence identification numbers: 1-53. For example, the primers are in vitro.

The term "isolated" does not include sequences that are present in the chromosomal content of vertebrates or vertebrate cells.

The nucleic acid, PCR primers or mixture may be provided in vitro, for example, mixed with a PCR buffer or reagent. In one example, the nucleic acids, primers, or mixtures of the invention are provided in a container, vial, test tube, petri dish, or PCR cell.

Optionally, the first isolated nucleic acid comprises (or consists of) a sequence that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to selected from the sequence identification number: 1 -47 is a sequence of the group. Optionally, the first isolated nucleic acid comprises (or consists of) a sequence selected from the group consisting of sequence identification numbers: 1-47.

75. The mixture of concept 74, wherein the first isolated nucleic acid comprises a sequence that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to selected from the sequence identification number: 1- A sequence of 17 in the group.

Optionally, the first isolated nucleic acid comprises a sequence selected from the group consisting of sequence identification numbers: 1-17.

76. The mixture of concept 74, wherein the first isolated nucleic acid comprises a sequence that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to selected from the sequence identification number: 18- A group of 26 in the group.

Optionally, the first isolated nucleic acid comprises a sequence selected from the group consisting of sequence identification numbers: 18-26.

77. The mixture of concept 74, wherein the first isolated nucleic acid comprises a sequence that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to selected from the sequence identification number: 27- A group of 47 in the group.

Optionally, the first isolated nucleic acid comprises a sequence selected from the group consisting of sequence identification numbers: 27-47.

78. The mixture of any one of concepts 74 to 77, wherein the second isolated nucleic acid comprises an antibody constant region sequence; optionally a sequence which is at least 90, 91, 92, 93, 94, 95, 96, 97 , 98, or 99% agree with a sequence selected from the group consisting of sequence identification numbers: 48 to 53.

Optionally, the second isolated nucleic acid comprises a sequence selected from the group consisting of sequence identification numbers: 48-53. Sequence identification numbers: 48-51 are sequences from the mouse constant region; sequence identification numbers: 52 and 53 are sequences from the human constant region (see Table 1).

79. The mixture of concept 75, wherein the second isolated nucleic acid comprises an antibody heavy chain constant region sequence; and optionally comprises a sequence which is at least 90, 91, 92, 93, 94, 95, 96, 97, 98 Or 99% identical (or 100% identical) sequence identification number: 48 or 49.

80. The mixture of concept 76, wherein the second isolated nucleic acid comprises an antibody κ chain constant region sequence; and optionally comprises a sequence which is at least 90, 91, 92, 93, 94, 95, 96, 97, 98 Or 99% agree (or 100% agree) with the sequence identification number: 50 or 51.

81. The mixture of concept 77, wherein the second isolated nucleic acid comprises an antibody lambda chain constant region sequence; and optionally a sequence which is at least 90, 91, 92, 93, 94, 95, 96, 97, 98 Or 99% agree (or 100% agree) with the sequence identification number: 52 or 53.

82. A nucleic acid mixture comprising a first isolated nucleic acid and a second isolated nucleic acid, wherein the nucleic acids are different and selected from a nucleic acid comprising a sequence, wherein the sequence is at least 90, 91, 92, 93 , 94, 95, 96, 97, 98, or 99% are identical (or 100% identical) are selected from a sequence in the group consisting of sequence identification numbers: 1-47.

In one example, the nucleic acids are PCR primers; in another embodiment, they include a homologous recombination vector for modifying an Ig locus or locus.

83. The mixture of idea 82, comprising a sequence selected from the group consisting of sequence identification numbers: 18-26, and a sequence at least 90, 91, 92, 93, 94, 95, 96, 97 , 98, or 99% agree (or 100% agree) with a sequence selected from the group consisting of sequence identification numbers: 18-26 and / or a sequence selected from the group consisting of sequence identification numbers: 27-47 By.

84. A mixture of concepts 82 or 83, wherein each of the first and second isolated nucleic acids is selected, and they are at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% consistent Yu (or 100% identical) is selected from a sequence in the group consisting of sequence identification numbers: 1-17.

85. A mixture as in concept 84, which contains at least 3 different isolated nucleic acids, each of which is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) ) Selected from a sequence in the group consisting of sequence identification numbers: 1-17.

86. The mixture of concepts 82 or 83, wherein each of the first and second isolated nucleic acids is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) Yu) is selected from a sequence in the group consisting of sequence identification number: 18-26.

87. The mixture of concept 84, which contains at least 3 different isolated nucleic acids, each of which is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) ) Is selected from a sequence in the group consisting of sequence identification number: 18-26.

88. The mixture of concepts 82 or 83, wherein each of the first and second isolated nucleic acids is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) Yu) is selected from a sequence in the group consisting of sequence identification numbers: 27-47.

89. The mixture of idea 84, which contains at least 3 different isolated nucleic acids, each of which is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or 100% identical) ) Is selected from a sequence in the group consisting of sequence identification numbers: 27-47.

90. The mixture of concepts 84 or 85, wherein the mixture comprises an antibody heavy chain constant region sequence; and optionally a sequence identification number: 48 or 49.

91. The mixture of concepts 86 or 87, wherein the mixture comprises an antibody kappa chain constant region sequence; and optionally a sequence identification number: 50 or 51.

92. The mixture of concepts 88 or 89, wherein the mixture comprises an antibody lambda chain constant region sequence; and optionally a sequence identification number: 52 or 53.

93. The method of any one of concepts 1 to 36, wherein step (c) is performed by PCR using one or more mixtures of any one of concepts 74 to 92.

94. The method of any one of concepts 48 to 56, wherein the method is performed by PCR using one or more mixtures as in any one of concepts 74 to 92.

95. A kit comprising one or more mixtures as in any one of concepts 74 to 92 and a device as in any one of concepts 36 to 39.

96. A method of amplifying a human variable region sequence library, the method comprising a. Providing a population of cells expressing a human variable region library, wherein the cells comprise a nucleotide sequence encoding the variable region; b. Using PCR And PCR template to copy several of the variable region-encoding nucleotide sequences; and c. To isolate, sequence, or identify one or more of the copied nucleotide sequences, or to implement the method of any one of concepts 1 to 36 Steps (d) and (e); wherein one or more of the templates of step (b) comprise a sequence that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to ( Or 100% identical) selected from a sequence of the group consisting of sequence identification numbers: 1-53.

97. The method of idea 96, wherein step (b) uses a mixture or mixtures of any one of ideas 74 to 92 as a PCR template.

98. The method of concept 96 or 97, wherein the cell line in step (a) is a sorted single cell (e.g., sorted into holes of one or more plates).

99. The method of concept 96 or 97, further comprising producing a human variable region using one of the replicated sequences obtained in step (c) (eg, as part of an isolated antibody chain or an isolated antibody for use in human medicine), and Optionally, a cell line expressing one of the human variable regions is produced.

The following optional features are applied to describe any configuration, aspect, embodiment or example of the present invention.

Optionally, the POI-encoding nucleotide sequence is operably linked to a promoter capable of driving the performance of the POI, wherein the promoter comprises a eukaryotic promoter that can be regulated by an activator or inhibitor. In another embodiment, the eukaryotic promoter is operably linked to a prokaryotic operator, and the eukaryotic cell optionally further comprises a prokaryotic repressor protein.

Optionally, each expression cassette contains a sequence encoding a marker, such as a selectable marker, such as a hygromycin resistance gene or encoding a fluorescent protein (e.g., the fluorescent protein is selected from the group consisting of DsRed, GFP, eGFP, CFP, eCFP, and YFP).

Optionally, one or more or all of the performance cassettes include first and second POI-encoding nucleotide sequences, such as tandem or as a double cistron cassette. In one example, the encoded POIs are different (eg, VH and VL of an antibody); in another example, they are different. In one example, 1, 2, 3, 4, 5, 6, or more POI-encoding nucleotide sequences.

In one example, the host cell or each host cell line is a CHO (Chinese Hamster Ovary) cell or a HEK293 cell.

For example, the protein of interest may be an antibody or a fragment thereof, a chimeric antibody or a fragment thereof, a ScFv or a fragment thereof, an Fc-tagged protein or a fragment thereof, a growth factor or a fragment thereof, a cytokine or A fragment thereof, or an extracellular domain of a cell surface receptor, or a fragment thereof.

Nucleic acid construct

The recombinant expression cassette (vector) may contain a DNA fragment encoding a synthetic or cDNA origin of a protein of interest, which is operably linked to a suitable transcription and / or translation regulatory element derived from a mammalian, viral or insect gene. Such regulatory elements include transcriptional promoters, enhancers, sequences encoding suitable mRNA ribosome binding sites, and sequences that control termination of transcription and translation. Mammalian expression cassettes may also contain non-transcribed elements, such as an origin of replication, other non-transcribed sequences pinched at the 5 'or 3 "end, and non-translated sequences at the 5' or 3 'end, such as splice donor and acceptor sites. A selectable marker gene that facilitates recognition of transfectants may also be incorporated.

Transcription and translation control sequences useful in transfection of vertebrate cells in expression cassettes may be provided by viral sources. For example, commonly used promoter and enhancer lines are derived from viruses such as polyoma virus, adenovirus 2, simian virus 40 (SV40), and human cytomegalovirus (CMV). Viral gene promoters, control and / or signal sequences may be used to drive performance if such control sequences are compatible with the host cell of choice. Non-viral cellular promoters may also be used (e.g., the β globulin and the EF-1α promoter), depending on the cell type in which the recombinant protein is to be expressed.

DNA sequences derived from the SV40 virus genome, for example, SV40 origin, early and late promoters, enhancers, splicing, and polyadenylation sites may be used to provide other genetic elements that appear to be useful for heterologous DNA sequences . Early and late promoter lines are particularly useful because both are easily obtained from SV40 virus with a fragment that also contains the origin of SV40 virus replication (Fiers et al. "Nature, 1978, 273: 113"). Smaller or larger SV40 fragments may also be used. Typically, a sequence line extending from the HindIII site towards the BglI site and located at about 250 origins of SV40 replication is included.

The bicistronic expression vectors for multiple transcript expression have been previously described (Kim S.K. and Wold B.J. in "Cell, 1985, 42: 129") and can be used in combination with one or more POI coding sequences.

Host cells and transfection

Optionally, eukaryotic host cell lines are used in the methods of the invention, for example they are mammalian host cells, including, for example, CHO cells or mouse cells.

The expressed protein (POI) is preferably secreted into the culture medium, depending on the selected nucleic acid sequence, but may also remain in the cell or be deposited in the cell membrane. Various mammalian cell culture systems may be employed to express recombinant proteins. Examples of suitable mammalian host cell lines include the COS-7 strain of monkey kidney cells, described by Gluzman in "Cell 23: 175" in 1981, and other cell lines capable of expressing a suitable vector, including, for example , CV-1 / EBNA (ATCC CRL10478), L cells, C127, 3T3, CHO, HeLa cells and BHK cell lines. Other cell lines developed for specific selection or scale-up protocols are also useful in conjunction with the methods and compositions provided herein. A preferred cell line is the CHO cell line named K1. To achieve the goal of mass production of recombinant proteins, the host cell line is optionally pre-adapted to the bioreactor medium where appropriate.

In this technique, several transfection experiments are known and reviewed in Kaufman's "Meth. Enzymology 185: 537" mid-1988. The chosen transfection experiment plan will depend on the type of host cell and the nature of the POI, and can be chosen based on routine experiments. The basic requirements of any such experimental program are first to introduce DNA encoding the protein of interest into a suitable host cell, and then to identify and isolate a host that has incorporated the heterologous DNA in a relatively stable, expressible manner cell.

One common method for introducing heterologous DNA into cells is calcium phosphate precipitation, for example, as described by Wigler et al. (Proc. Natl. Acad. Sci. USA 77: 3567, 1980). DNA introduced into a host cell by this method is often rearranged, making this procedure useful for co-transfection of independent genes.

The fusion of polyethylene-induced bacterial protoplasts with mammalian cells (Schaffner et al., "Proc. Natl. Acad. Sci. USA 77: 2163", 1980) is another useful method for introducing heterologous DNA. Protoplast fusion experiments often produce multiple copies of plastid DNA that are incorporated into the mammalian host cell genome, and this technique requires the selection and amplification to be labeled on the same nucleic acid as the POI.

Electroporation can also be used to introduce DNA directly into the cytoplasm of a host cell, for example, such as by Potter et al. (Proc. Natl. Acad. Sci. USA 81: 7161, 1988) or Shigekawa et al. (BioTechniques , 6: 742, 1988). Unlike protoplast fusion, electroporation does not require a selectable marker to be on the same nucleic acid as the POI.

Recently, several agents useful for introducing heterologous DNA into a mammalian cell have been described. These include Lipofectin ™ reagent and Lipofectamine ™ reagent (Gibco BRL, Gaithersburg, Maryland). Both of these agents are commercially available reagents used to form lipid-nucleic acid complexes (or liposomes), both of which, when administered to cultured cells, promote the uptake of nucleic acids into the cells.

A method for amplifying the POI is also desirable for the performance of the recombinant protein and typically involves the use of a selectable marker (reviewed in Kaufman above). Cytotoxic drug resistance is the trait most commonly used as a selection marker and can be a dominant trait (e.g., can be used independently of the host cell type) or a recessive trait (e.g. Useful in host cells) either result. Several amplifiable markers are suitable for use in the expression vectors of the present invention (eg, as described in "Molecular Biology: A Laboratory Manual, Cold Spring Harbor Laboratory, NY, 1989; pgs 16.9-16.14" by Maniatis).

Useful selectable markers for gene amplification in drug-resistant mammalian cells are shown in Table 1 of Kaufman, RJ above, and include DHFR-MTX resistance, P-glycoprotein, and multiple drug resistance (MDR)-various Lipophilic cytotoxic agents (such as doxorubicin, colchicine, vincristine) and adenosine deaminase (ADA) -Xyl-A or adenosine with 2'-deoxycoformin.

Other dominant selectable markers include antibiotic resistance genes derived from microorganisms, such as neomycin, kanamycin, or hygromycin resistance. However, these selectable markers have not been shown to be zoomable (Kaufman, R.J. above). For mammalian hosts, there are several suitable selection systems ("pgs 16.9-16.15" by Maniatis, supra). A co-transfection experiment using two dominant selection markers has also been described (Okayama and Berg, Mol. Cell Biol 5: 1136, 1985).

In this technique, useful regulatory elements previously described or known can also be included in the nucleic acid construct for transfecting mammalian cells. The chosen transfection experiment plan and the elements selected for use in it will depend on the type of host cell used. Those skilled in the art know many different experimental plans and host cells, and can choose an appropriate system for the expression of a desired protein based on the requirements of the cell culture system used.

One aspect provides a pharmaceutical composition comprising an isolated POI (such as an antibody, chain or variable domain) and a diluent, excipient or carrier, optionally wherein the composition is contained in an IV container ( For example, and IV bag) or attached to a container of the IV syringe, and wherein the POI has been isolated from a host cell or host cell population of the present invention.

One aspect provides the use of the POI of the present invention in the manufacture of a medicament for treating and / or preventing a disease or condition in a patient, such as a human.

It should be understood that the specific embodiments described herein are shown by way of example, and not as a limitation of the present invention. The main features of the present invention can be adopted in various embodiments without departing from the scope of the present invention. Using no more than conventional research, those skilled in the art will understand or be able to ascertain the many equivalents of the specific procedures described herein. Such equivalents are considered to be within the scope of the invention of the present invention and are covered by the claims. All publications and patent applications mentioned in this specification are manifested as the level of a skilled person familiar with the art to which the present invention belongs. All publications and patent applications are hereby incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually shown as incorporated for reference. The word "a" or "an" when used in conjunction with the terms "including" in these claims and / or this specification may mean "an", but it also conforms to "one or more", "at least one The meaning of "and" one or more. In such claims, the use of the term "or" is used to mean "and / or" unless expressly indicated to mean only alternatives or such alternatives are mutually exclusive, although this disclosure supports Refers to one of the definitions of "and / or". Throughout this application, the term "about" is used to indicate a value that includes variations in error inherent in the device or method employed to determine the value, or variations that exist among such subjects.

Example 1

The B-cell colony technology of the present invention includes three main steps-isolation of antigen-specific single B cells or ASCs derived from the spleen, lymph nodes, and bone marrow by means of corresponding cell markers; antibody sequence preservation and performance cassettes derived from single cells Scale up; recombinant antibodies are expressed in mammalian cells. The flowchart is shown in Figure 1B. The details of each step are described below

Example 1A: Isolation of antigen-specific single cells

Antigen-specific cells include memory / GC cells with membrane-bound antibodies and antibody-secreting plasma cells. A small group of cell surface markers were used to define and mark mouse memory / GC cells (CD19; IgM; IgD; CD38; CD95) (Figure 2). Antigen-specific cell lines use fluorescent marker-soluble antigen staining (for example, any small molecule fluorophore that can be detected by a cell sorting system, such as Alexa-488, Alexa-647, Pacific Blue, R- Phycoerythrin, luciferin isothiocyanate or isophycocyanin, optionally conjugated to a cyanine dye, such as Cy7), or cell surface antigen stained in a virus-like particle (VLP). Figure 2 is an example of marker antigen-specific memory / GC cells in the spleen of OVA-immunized mice. More than 10,000 OVA-specific memory / GC IgG cells can be sorted from one spleen. Single cell sorting lines were performed using a BD influx flow cytometer equipped with an automated cell deposition unit. FACS-sorted cell lines were deposited into a 96-well PCR plate with lysis buffer for the next step.

Generally, antigen-specific GC (reproductive center) or memory B cells can be captured by marker antigens because they are manifested as transmembrane antibodies on the cell surface. Plasmablasts or plasma cells, on the other hand, are not considered to be easily captured by marker antigens because of their dominant manifestation of secreted antibodies. We then attempted to isolate ASPC using a fluorescently labeled antigen and anti-CD138 to sort the cells from the remainder of the cell population using FACS (Figure 2). As shown in Figure 2, in the ELISPOT assay, most of the isolated antigen-specific plasma cells or plasmablasts showed that they were antigen-specific ASCs, but not those of the same type of cells that remained. This proves that the cell sorting method using fluorescent-labeled antigens can effectively capture all antigen-specific ASCs, possibly through residual transmembrane antibodies or temporary anchored antibodies on the cell surface.

The fluorescently labeled antigen can be replaced with a VLP having a recombinant antigen on its surface. These VLPs are produced from CHO cells, KEK cells, MEF (mouse embryonic fibroblasts) or other mammalian cell lines, and are accompanied by recombinant antigens, gag proteins of retroviruses, and MA-GFP (p15- GFP fusion protein). The gag appearance allowed VLPs to sprout from the cells, and MA-GFP marked the VLPs for fluorescent detection. Both gag and MA-GFP proteins bind to the inner surface of the plasma membrane, and the recombinant antigen is on the surface of the VLP. The antigenic line on the VLP is presented in a native form that is expressed directly from recombinant cells without any purification or modification steps. A native form of an antigen should provide all the natural epitopes that greatly assist in the selection of neutralizing antibodies. The high density of the antigens on the VLP increases the signal / noise ratio for detecting cells expressing antigen-specific antibodies on the cell surface and greatly facilitates this sorting step. The recombinant VLPs can be generated with the expression of different fluorescent proteins, such as MA-CFP or MA-YFP. Cells that exhibit high affinity binders, cross-reactive conjugates, or homolog-specific conjugates using multiplexed VLPs with different antigens and different fluorescent proteins can be selected. The cells exhibiting high-affinity conjugates can be selected by cells with a relatively high affinity matrix (affinity matrix = ratio of binding activity to low density antigen VLP to high density antigen VLP). Cells that exhibit cross-reactive conjugates for heterologous or different antigens (against the isolation of 2-in-1 or bispecific antibodies) can be selected by binding to cells of different types of VLPs at the same time. Cells expressing homolog-specific conjugates can also be selected by cells that bind to specific antigens but not their homologs.

Example 1B: High-throughput recovery of antibody sequences from a single cell

A fast, efficient, and high-throughput method was developed for the production of antibodies from individual B cells without the need for any molecular colonization steps. This method allows us to generate Ig-expressing constructs from the amplified variable gene segments of the heavy and light chains of a single cell (Figure 3). Throughout the entire PCR program, the heavy and light chains derived from a single cell were amplified in the same hole.

The sequence of the antibody V region was recovered by RT-PCR and two rounds of PCR following the procedure below. Sorted single cell trays stored at -80 ° C were thawed on ice and centrifuged briefly before use. The plates were grown in a thermal cycler for 5 minutes at 65 ° C and indefinitely at 4 ° C. A 6 μL mixture of primer, Superscript III, dNTP, RNase inhibitor and buffer was added to each well and mixed by pipetting. The dishes were centrifuged briefly and incubated at 50 ° C for 60 minutes. Specific primer lines for the heavy and light chain constant regions are used to amplify variable gene segments derived from a single cell. Gene-specific reverse primers used to amplify the κ, λ, and γ chains were γRT1, κRT1, and λRT3.

This first round of PCR was performed with a forward V gene-specific primer having a human cytomegalovirus (hCMV) promoter fragment at its 5 'end and a reverse constant region-specific primer. The product from the RT-PCR was used as a template for the first PCR. The PCR product contains a variable immunoglobulin region and a portion of the constant region. For the first PCR, the cycling conditions included an initial denaturation step for 30 minutes at 98 ° C, followed by 10 minutes at 98 ° C, 30 minutes at 72 ° C to 60 ° C, and 30 minutes at 72 ° C, with each subsequent 13 decremental cycles of 1 ° C decrease in adhesion step; 20 cycles of 98 ° C for 10 minutes, 60 ° C for 30 minutes, and 72 ° C for 30 minutes, followed by a final extension at 72 ° C for 2 minutes and maintained at 4 ° Indefinitely.

In the second round of PCR, a universal forward primer line adhered to the hCMV tag was used with a reverse nested primer directed to the constant region. The 1 μL product from the first PCR was used as a template for the second nested PCR. For the second PCR, the cycling conditions include an initial denaturation step for 30 minutes at 98 ° C, followed by 20 cycles of 98 ° C for 10 minutes, 68 ° C for 30 minutes, and 72 ° C for 30 minutes; a final extension at 72 It was held at 2 ° C for 2 minutes and kept at 4 ° C indefinitely. One third of the PCR products of the second round were run on a 1% agarose gel to check the recovery of RT and two rounds of PCR steps from a single cell-derived antibody sequence. Since the primers for heavy and light chains are mixed into the same hole, the PCR product contains two bands representing the VDJ region of the heavy chain and the VJ region of the light chain. The expected size of the PCR product is ~ 700 bp for the κ and λ light chains and ~ 500 bp for the γ heavy chain (Figure 4a).

For the expression of antibodies in mammalian cells, the amplified product was then bridged with a linear Ig-cassette bridge with a 5 'PB LTR-CMV promoter and a constant region-polyadenylation signal-3' PB LTR (Figure 3). The Ig-cassette contains all necessary elements for expression of the antibody, including the CMV promoter, the immunoglobulin chain constant region, and the poly (A) signal. In addition, the cassette has a long overlapping region of CMV and constant region homologues at its ends. The 2 μL product from the second round of PCR was used as a template for this bridge PCR. For this bridge PCR, the cycling conditions include an initial denaturation step for 30 minutes at 98 ° C, followed by 5 cycles of 98 ° C for 10 minutes, 68 ° C for 30 minutes, and 72 ° C for 2 minutes; and 98 ° C for 10 minutes. 25 cycles of 30 minutes at 60 ° C for 30 minutes and 72 ° C for 2 minutes; the last one is extended at 72 ° C for 2 minutes and maintained at 4 ° C indefinitely. One third of the bridge PCR product was run on a 1% agarose gel to check the recovery of the bridge PCR. The expected size of the PCR product is ~ 2600bp for the κ and λ light chains, and ~ 3100bp for the γ heavy chain (Figure 4b).

This bridging step allows bridging all expression elements together with the PB LTR to form the PB transposon with the heavy and light chain expression genes. Regardless of the isotype of the mouse antibody, mouse IgG1, IgG2a, IgG2b, IgG3, or any variant of human IgG1, IgG2, IgG3, IgG4, or constant region can be administered in this bridging step to reformat the Fc format . The method applied in this technique does not require any purification steps and can be widely automated. For different cell populations, the overall recovery rate for the B-cell technology (BCT) for cell sorting and single-cell PCR is about 38-71% (see Table 3).

Example 1C: Sequence analysis by clusters

This second round of PCR products was sent for sequencing. The nucleotide sequences were determined using an Applied Biosystems 373 DNA sequencer. These sequences were analyzed by the Kymab seq-utils program (Lee E.C. et al. In "Nature Biotechnol., 2014, 32: 356-363"). The program predicts high mutations in the germline sequence and the analyzed IG sequence. The variable immunoglobulin region includes a VDJ region of an immunoglobulin nucleotide sequence, for a heavy chain gene, and a VJ region of an immunoglobulin nucleotide sequence, for Igκ and Igλ. A breeding family is generally defined by the use of related immunoglobulin heavy and / or light chain V (D) J sequences from two or more samples. The related immunoglobulin heavy chain V (D) J sequence can be identified by the shared use of the V (D) J gene segment that it encodes in the genome (Figure 5).

Within a breeding family, there are generally subfamilies that change based on shared mutations that can occur within their V (D) J segments during B-cell genetic recombination and somatic high mutations. Breeders with different V (D) J segments often exhibit different binding characteristics. In addition, clones with the same V (D) J segment but different mutations exhibit different binding characteristics. B cells undergo somatic hypermutation, in which random changes in the nucleotide sequence of the antibody gene are made, and B cells whose antibodies have higher affinity are selected by B cell lines (Figure 6). If low-affinity clones from the same lineage have a neutralizing function, the titer is usually increased in those with more mutations to obtain higher affinity.

Example 1D: Monoclonal antibody production from a single cell

The final PCR step amplifies the linear expression cassette encoding the heavy and light chains. The amplified cassette targeting heavy and light chains, and the PB transposase (PBase) expression vector system were co-transfected into mammalian cell lines without purification and colonization. Supernatants with transient or stable antibody performance are then collected at corresponding time points. Transfection of traditional expression vectors may result in the integration of the concatemer into the genome, and the incorporated gene line is subject to silence. PB transposon-mediated expression provides a major advantage to the high and stable expression of transfected genes, as multiple copies (10-100) of PB transposons can be translocated and incorporated into the transcriptionally active region The genome allows high-volume expression of antibodies (Figure 7).

For transient expression, the transfection line of the bridge PCR product and the PBase expression vector was performed using Lipofectamine 2000 according to the manufacturer's experimental plan. Transfection was performed in a 96-well deep-well plate. Briefly, HEK293 cell lines were cultured in DMEM + 10% ultra-low IgG FBS (Invitrogen) to prevent bovine IgG from competing with secreted human IgG during the downstream protein A purification step. For 96-well plate transfection, each well was seeded with 5 × 105 cells in 500 μL of medium the previous day and allowed to grow to 1 × 106 cells the next day. 25 μL of the 30 μL bridge PCR product and 100 ng of PBase vector were incubated in Optimem medium at a final volume of 70 uL. Both were incubated for 10 minutes. Lipofectamine 2000 was then mixed with the PCR product by gently pipetting, and incubated for 15 minutes before adding to HEK293 cells, and mixed gently. The culture supernatant was collected on the 8th day after transfection and used for the following screening. The IgG concentration of the supernatant containing the antibody of interest was determined by IgG ELISA (Figure 8). The concentration of the expressed antibody is comparable to the concentration that we normally obtain from hybridoma technology, which is sufficient for screening of the most downstream antibody binding ability or functional detection. Depending on the cell population, the overall hit rate for IgG recognition by B-cell technology through cell sorting is 36% -71% (Table 3).

Example 1E: Antibody Binding Screening Detection Using LI-COR's Odyssey NIR scanning

Performance antibodies derived from HEK293 cells transfected with B-cell technology (BCT) were first screened for their ability to bind to the antigen of interest using LI-COR Odyssey near-infrared scanning, and then positively selected strains resonated by surface plasmon (ProteOn XPR36, BioRad) was screened for its apparent affinity (see below).

The antigen-specific antibody system produced by B cells was identified by fluorescent screening. Using a Multidrop instrument, each well of a transparent 384-well flat-bottom plate was seeded in 80 μL of F12 medium (1.25 × 10 ⁵ cells / mL) containing 10% (v / v) FBS and inoculated 1 × 10 ⁴ Attached CHO cells, wherein the CHO cell line is stably transfected with a gene encoding a human transmembrane antigen. The cell lines were incubated overnight in a CO ₂ incubator at 37 ° C. The next day, the medium was removed by suction, and 45 μL of the LI-COR IRDye 800CW anti-mouse antibody system was added at 500ng / mL + 5mM DRAQ5 (LI-COR), which was in FACS buffer ( PBS + 1% BSA + 0.1% NaN ₃ ) diluted 1: 25000. 5 μL of BCT supernatant, 5 μL of control antibody (2 μg / mL) in HEK293 medium, or 5 μL of mouse IgG1 control antibody in HEK293 medium (Sigma, 2 μg / mL) was added using a FluidX liquid dispenser. The plates were incubated at 4 ° C for 1 hour, and the culture medium was aspirated. The reaction line was stopped, and the cell line was fixed by adding 25 μL of paraformaldehyde per well and incubating at RT for 15 minutes. The dish was washed twice with 100 μL of PBS, and the washing solution was removed by rubbing on a paper towel. The plates were scanned using a LI-COR Odyssey classic instrument. Depending on the cell population, the overall hit rate for antigen-specific recognition of BCTs sorted by cells was 25% -61% (Table 3).

Example 1F: Affinity measurement by SPR using antibody capture method

Positive clones expressing antigen-specific antibodies were then screened for apparent affinity by surface plasmon resonance. Anti-mouse IgG (GE Healthcare / Biacore) was coupled to the GLM via primary amine coupling. The GLM wafer (BioRad) was activated using NHS / EDAC, and the anti-mouse IgG was coupled to the activated surface and then blocked with 1M ethanolamine. Immobilization is performed individually at either room temperature or 37 ° C in either HBS-EP (Teknova) or HBS-N (GE Healthcare / Biacore). An anti-mouse IgG surface on this GLM wafer was used to directly capture the antibody of interest. For kinetic analysis, 5 concentrations of analyte system were used (256nM, 64nM, 16nM, 4nM, and 1nM). For data analysis, the combined spectrum was referenced using an internal "interspot" uniquely referenced to the ProteOn XPR36, where the ProteOn XPR36 was double-referenced using a buffer injection spectrum. Finally, the data was analyzed using ProteOn XPR36 analysis software's inherent 1: 1 model.

FIG. 9 is an example of SPR data of antibodies derived from the ovalbumin-immunized Kymouse® using the single B-cell technology of the present invention. About two-thirds of the tested antibodies showed evidence of binding to the antigen, accompanied by range-differentiating differential binding affinity and kinetics. Changes in binding characteristics revealed that the cell sorting procedure is effective in capturing disparate quality antibodies. Regardless of the scale of this experiment (2 animals), many high-affinity anti-systems in this low nM to low pM range were isolated, verifying the efficiency of affinity maturation.

Figure 10 shows the apparent affinities of antibodies for two different Kymab target antigens. A range of conjugates (hollow) and functional mixtures (solid) are detected with the highest affinity detected in the pico-molar range. This confirms that the single B cell colony technology of the present invention is a powerful tool in the recognition and acquisition of high affinity and functionally competent antibodies.

As used in this specification and in the claims (etc.), the words "is being included" (and any form of being included, such as "including" and "including"), "is being" (and any form of being , Such as "having" and "having"), "including" (and any form of including, such as "including" and "including"), or "including" (and any form of including, such as "containing "And" containing ") are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

The term "or a combination thereof" as used herein means all permutations and combinations of the items listed before the term. For example, "A, B, C, or a combination thereof is intended to include at least one of the following: A, B, C, AB, AC, BC, or ABC, and if the order is important in a particular context, also Includes BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing this example, explicitly included are repeated combinations containing one or more items or entries, such as BB, AAA, MB, BBC, AAABCCCC, CBBAAA , CABABB, and the like. Those skilled in the art will understand that typically there is no limit to the number of items or entries in any combination, unless otherwise apparent from the context.

Any part of this disclosure may be read in conjunction with any other part of this disclosure, unless otherwise obvious from the context.

In view of the content of this disclosure, all the components and / or methods disclosed and claimed herein can be made and performed without undue experimentation. Although the composition and method of the present invention have been described in terms of preferred embodiments, it will be apparent to those skilled in the art that variations may be applied to the composition and / or method, and the steps of the method are described herein Or in the order of the steps without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

<110> KYMAB LIMITED

<120> Performance vector production and high-throughput cell screening

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<213> wise man

<220>

<223> Human kappa chain constant region specific sequence.

<400> 50

<210> 51

<211> 29

<212> DNA

<213> wise man

<220>

<223> Human kappa chain constant region specific sequence.

<400> 51

<210> 52

<211> 36

<212> DNA

<213> wise man

<220>

<223> Human kappa chain constant region specific sequence.

<400> 52

<210> 53

<211> 25

<212> DNA

<213> wise man

<220>

<223> Human kappa chain constant region specific sequence.

<400> 53

<210> 54

<211> 35

<212> DNA

<213> wise man

<220>

<223> CMV promoter sequence

<400> 54

<210> 55

<211> 313

<212> DNA

<213> wise man

<220>

<223> PiggyBac (PB) transposable element inverts 5 'end repeat element

<400> 55

<210> 56

<211> 235

<212> DNA

<213> wise man

<220>

<223> PiggyBac (PB) transposable element is inverted at the 3 'end repeat element

<400> 56

<210> 57

<211> 594

<212> PRT

<213> wise man

<220>

<223> Wild-type piggyBac transposase

<400> 57

<210> 58

<211> 594

<212> PRT

<213> wise man

<220>

<223> Highly active piggyBac transposase

<400> 58

Claims (12)

A process for producing encoding a cell-V _H sequences and V _L sequences of the antibody binding site library (a repertoire) to include, the method comprising: a) providing a performance of an antibody binding site library cell populations, which the cell line from Isolated from one or more animals and comprising B cells, germinal centre cells, memory B cells, antibody-secreting cells, plasma cells, or plasmablasts; b) by binding the antibodies to a site Bind to an antigen of interest to sort the cell population to produce a single cell population that is sorted, each cell contains a nucleic acid encoding a different antibody binding site, and each sorted cell line is in a different Provided in a container; c) using PCR to amplify nucleic acids contained in the sorted single cell population to generate a sorted amplified nucleic acid library encoding antibody binding sites, wherein each antibody binding site The V _H and V _L sequences are amplified in the same container; d) the sorted and amplified antibody binding site encoding nucleic acid derived from step (c) is modified to generate a sorted performance cassette library, each One container pack A cassette of a first type and a second type of cassette, the cassette comprising a first type of coding derived from a single cell of the nucleotide sequence of the V _H sequence of a binding site of the antibody with one or more A regulatory element for expressing the _VH sequence of the antibody binding site, the second type of cassette contains a nucleotide sequence encoding a _VL sequence of an antibody binding site derived from the single cell and one or more A regulatory element for expressing the V _L sequence of the antibody binding site, wherein the V _H and V _L sequences of each antibody binding site are modified in the same container; and e) the antibody is transfected from the cassette library Binding site performance cassette to a sorted host cell population, while maintaining the antibody binding site performance cassette sorting and generating a sorted host cell bank representing a sorted library of antibody binding sites, where The sorted host cell bank is capable of expressing the antibody binding site library.     The method of claim 1, wherein the sorted performance cassette in step (e) is transplanted in batches to the sorted host cells.         The method of claim 2, wherein the sorted performance cassette in step (e) is not purified when transfected.         The method of any one of claims 1-3, wherein (i) the sorted performance cassettes generated in step (d) are provided in a plurality of containers which are fixed relative to each other, wherein, Each container contains a separate type of performance cassette, so that the relative position of the performance cassettes relative to each other is predetermined; and (ii) the performance cassettes are transferred to the sorted in step (e) The relative position of the expression cassettes is maintained in the host cells.         The method of any one of claims 1-3, wherein (i) the performance cassette library generated in step (d) is sorted by providing a plurality of containers, each of which is contained in step ( b) the antibody binding site coding sequence of the sorted single cell; (ii) the sorted host cell lines of step (e) are provided in several containers, and (iii) the performance cassette systems Transplanted into the sorted host cells in step (e) such that the host cells in each individual container encode only antibody binding sites derived from the single cells sorted in step (b) Sequence mixing.         The method of any one of claims 1-3, wherein step (b) is performing cell sorting using FACS.         The method of claim 6, wherein the FACS for cell sorting is fluorescent FACS.         The method of any one of claims 1-3, wherein the homologous system is a fluorescently labeled antigen; or a type of virus particle (VLP) comprising a performance antigen on the surface, and further comprising a fluorescently labeled protein .         The method of any of claims 1-3, wherein step (d) comprises modifying the amplified nucleic acid by combining with a predetermined sequence such that the predetermined sequence sandwiches the antibody binding sites of the nucleic acids The 5 'and / or 3' end of the coding nucleotide sequence; wherein the modification places a regulatory element and / or a transposer element to pinch the 5 'and / or 3' end of the antibody binding site coding nucleotide sequence.         The method of any one of claims 1-3, wherein step (e) comprises incorporating the antibody binding site expression cassette genes into individually used to express the individual antibody binding sites In the genome of the host cell, the gene incorporation is performed using a predetermined genomic nucleotide sequence motif for inserting the expression cassettes into the genome of the individual cell.         The method of claim 10, wherein the gene incorporation is performed by transposon-mediated integration.         The method of any of claims 1-3, wherein the modification in step (d) is performed using bridge PCR to produce a performance cassette containing 5'- and 3'-terminal transposable elements, wherein Between the transposable elements, there is an antibody binding site coding nucleotide sequence and a regulatory element for the expression of the antibody binding site.